Multi-area layer-resolved spiking network model of resting-state dynamics in macaque visual cortex

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Accession:262457
See https://inm-6.github.io/multi-area-model/ for any updates.
References:
1 . Schmidt M, Bakker R, Shen K, Bezgin G, Diesmann M, van Albada SJ (2018) A multi-scale layer-resolved spiking network model of resting-state dynamics in macaque visual cortical areas. PLoS Comput Biol 14:e1006359 [PubMed]
2 . Schmidt M, Bakker R, Hilgetag CC, Diesmann M, van Albada SJ (2018) Multi-scale account of the network structure of macaque visual cortex. Brain Struct Funct 223:1409-1435 [PubMed]
3 . Schuecker J, Schmidt M, van Albada SJ, Diesmann M, Helias M (2017) Fundamental Activity Constraints Lead to Specific Interpretations of the Connectome. PLoS Comput Biol 13:e1005179 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Connectionist Network;
Brain Region(s)/Organism: Neocortex;
Cell Type(s): Abstract integrate-and-fire leaky neuron with exponential post-synaptic current;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEST;
Model Concept(s): Spatio-temporal Activity Patterns; Activity Patterns; Connectivity matrix; Synchronization; Multiscale;
Implementer(s): Schmidt, Maximilian [schmidt.maximilian at posteo.de]; Schuecker, Jannis ; van Albada, Sacha Jennifer [s.van.albada at fz-juelich.de];
from helpers import datapath

rule all:
    input:
        'Fig1_model_overview.eps',
        'Fig2_anatomy.eps',
        'Fig3_construction.eps',
        'Fig4_connectivity.eps',
        'Fig5_cc_laminar_pattern.eps',
        'Fig6_connectivity_measures.eps',
        'Fig7_community_structure.eps',
        'Fig8_laminar_paths.eps'

rule VisualCortexData:
    output:
        os.path.join(datapath, 'viscortex_processed_data.json')
    shell:
        'python ../../multiarea_model/data_multiarea/VisualCortex_Data.py'

rule Fig2_anatomy:
    output:
        'Fig2_anatomy.eps'
    input:
        os.path.join(datapath, 'viscortex_processed_data.json'),
        os.path.join(datapath, 'viscortex_raw_data.json')
    shell:
        'python3 Fig2_anatomy.py'

rule Fig3_construction:
    output:
        'Fig3_construction.eps'
    shell:
        'python3 Fig3_construction.py'

rule Fig4_connectivity:
    output:
        'Fig4_connectivity.eps'
    shell:
        'python3 Fig4_connectivity.py'

rule Fig5_cc_laminar_pattern:
    output:
        'Fig5_cc_laminar_pattern.eps'
    shell:
        'python3 Fig5_cc_laminar_pattern.py'

rule Fig6_connectivity_measures:
    output:
        'Fig6_connectivity_measures.eps'
    shell:
        'python3 Fig6_connectivity_measures.py'

rule Fig7_community_structure:
    output:
        'Fig7_community_structure.eps'
    shell:
        'python3 Fig7_community_structure.py'

rule Fig8_laminar_paths:
    output:
        'Fig8_laminar_paths.eps'
    shell:
        'python3 Fig8_laminar_paths.py'

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