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https://github.com/bluebrain/molsys-metabolicmodel

https://github.com/bluebrain/molsys-metabolicmodel

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
  • ✓
    codemeta.json file
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    .zenodo.json file
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    DOI references
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    Scientific vocabulary similarity
    Low similarity (11.4%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: BlueBrain
  • License: apache-2.0
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 21.1 MB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Created over 1 year ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

MetabolicModel Project

Repository Overview

This repository is organized into two main directories related to the research on multiscale electro-metabolic modeling of rat neocortical circuits.

1. EnergyCostMultiscaleProject

This folder contains the simulation setup and configuration files related to the project:
"Energy costs and efficiency of biological intelligence."
contributors: J. Coggan, S. Farina, J. King, P. Kumbhar and D. Keller

Contents include:

  • Simulation configuration files:
    • simulation_config.json
    • node_set.json
    • circuit_config.json
  • Example batch scripts (simulation.sbatch)
  • Script to compute the Energy Usage using the data obtained from the two simulations in the repository
  • Instructions for running the simulations

2. Multiscaleelectrometabolicratneocortex

This folder contains the code and information related to the article:
"A Multiscale Electro-Metabolic Model of a Rat Neocortical Circuit Reveals the Impact of Ageing on Central Cortical Layers"
by Sofia Farina, Alessandro Cattabiani, Darshan Mandge, Polina Shichkova, James B. Isbister, Jean Jacquemier, James G. King, Henry Markram, and Daniel Keller.

Contents include:

  • Figures and data analysis scripts
  • Electrical models of the neurons
  • Julia code for the Young and Aged metabolic simulations
  • Simulation configuration files:
    • simulation_config.json
    • node_set.json
    • circuit_config.json
  • Instructions for running the simulations and Jupyter Notebooks

Instructions

Both projects use Multiscale Orchestrator. You can find the detailed setup and usage instructions in the official MultiscaleRun documentation and on the MultiscaleRun GitHub repository. More details specific to each project can be found in the README files within each respective folder.

The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology.

Copyright (c) 2024 Blue Brain Project/EPFL

Owner

  • Name: The Blue Brain Project
  • Login: BlueBrain
  • Kind: organization
  • Email: bbp.opensource@epfl.ch
  • Location: Geneva, Switzerland

Open Source Software produced and used by the Blue Brain Project

GitHub Events

Total
  • Watch event: 1
  • Public event: 1
  • Push event: 4
  • Fork event: 1
Last Year
  • Watch event: 1
  • Public event: 1
  • Push event: 4
  • Fork event: 1

Dependencies

Multiscale_electrometabolic_ratneocortex/requirements.txt pypi
  • ArchNGV ==3.0.3
  • Jinja2 ==3.1.4
  • MarkupSafe ==2.1.5
  • MorphIO ==3.3.6
  • NEURON ==8.2.4
  • Pillow ==10.0.1
  • PyWavelets ==1.4.1
  • PyYAML ==6.0.1
  • Pygments ==2.16.1
  • annotated-types ==0.6.0
  • asttokens ==2.4.0
  • attrs ==23.1.0
  • backcall ==0.2.0
  • bluecellulab ==2.6.36
  • bluepysnap ==3.0.1
  • cached-property ==1.5.2
  • certifi ==2023.11.17
  • charset-normalizer ==3.3.2
  • click ==8.1.7
  • comm ==0.1.4
  • contourpy ==1.1.1
  • cramjam ==2.8.3
  • cycler ==0.12.1
  • debugpy ==1.8.0
  • decorator ==5.1.1
  • deprecation ==2.1.0
  • efel ==5.5.7
  • executing ==2.0.0
  • fastparquet ==2024.2.0
  • find-libpython ==0.3.1
  • fonttools ==4.43.1
  • fsspec ==2024.9.0
  • h5py ==3.10.0
  • idna ==3.4
  • imageio ==2.33.0
  • importlib-metadata ==6.8.0
  • importlib-resources ==6.1.0
  • ipykernel ==6.25.2
  • ipython ==8.12.3
  • ipywidgets ==8.1.1
  • jedi ==0.19.1
  • joblib ==1.4.2
  • jsonschema ==4.19.1
  • jsonschema-specifications ==2023.7.1
  • jupyter_client ==8.3.1
  • jupyter_core ==5.3.2
  • jupyterlab-widgets ==3.0.9
  • kiwisolver ==1.4.5
  • lazy_loader ==0.3
  • libsonata ==0.1.25
  • matplotlib ==3.7.5
  • matplotlib-inline ==0.1.6
  • more-itertools ==10.1.0
  • morph-tool ==2.9.1
  • neo ==0.13.3
  • nest-asyncio ==1.5.8
  • networkx ==3.1
  • neurom ==3.2.4
  • nptyping ==2.5.0
  • numpy ==1.22.0
  • packaging ==23.2
  • pandas ==2.0.3
  • parso ==0.8.3
  • patsy ==0.5.6
  • pexpect ==4.8.0
  • pickleshare ==0.7.5
  • pkgutil_resolve_name ==1.3.10
  • platformdirs ==3.11.0
  • prompt-toolkit ==3.0.39
  • psutil ==5.9.5
  • ptyprocess ==0.7.0
  • pure-eval ==0.2.2
  • pyarrow ==17.0.0
  • pydantic ==2.6.3
  • pydantic_core ==2.16.3
  • pynrrd ==1.0.0
  • pyparsing ==3.1.1
  • python-dateutil ==2.8.2
  • pytz ==2023.3.post1
  • pyzmq ==25.1.1
  • quantities ==0.15.0
  • referencing ==0.30.2
  • requests ==2.31.0
  • rpds-py ==0.10.6
  • scikit-image ==0.21.0
  • scikit-posthocs ==0.8.1
  • scipy ==1.10.1
  • seaborn ==0.13.2
  • six ==1.16.0
  • stack-data ==0.6.3
  • statsmodels ==0.14.1
  • tabulate ==0.9.0
  • tifffile ==2023.7.10
  • tornado ==6.3.3
  • tqdm ==4.66.1
  • traitlets ==5.11.2
  • trimesh ==4.0.4
  • typing_extensions ==4.8.0
  • tzdata ==2023.3
  • urllib3 ==1.26.18
  • vascpy ==0.1.1
  • voxcell ==3.1.6
  • wcwidth ==0.2.8
  • widgetsnbextension ==4.0.9
  • xmltodict ==0.13.0
  • zipp ==3.17.0