Community Involvement

 

On each of the model pages, you will find resources available, links to the Brain Simulation Platform where you can find the use cases and tools, and the latest publications from the teams.  

Here we list, the types of data that our models will be able to consume in the short-term to near future. If you would like to contribute to our collaborative model building efforts and could contribute any data, we would be happy to hear from you. You can directly contact the person listed under each model section below.

 

Signalling Cascades

CaMKII and Endocannabinoid Cascades

Type of data

Species

Brain region

Cell type

Target sets of receptors (NMDA, AMPA, mGluR5, CB1, M1)

-

Basal ganglia, cerebellum, hippocampus, somatosensory cortex

Principal neurons

 

Target sets of signalling molecules (e.g. Cam, CaMKII, Gq-proteins, PLC, DAGL, PKC, etc.)

-

Basal ganglia, cerebellum, hippocampus, somatosensory cortex

Principal neurons

 

Amounts of the target molecules above

-

Basal ganglia, cerebellum, hippocampus, somatosensory cortex

Principal neurons

 

Co-localisation of CB1R and other receptors pre- and postsynaptically, co-localisation of Cav1.3 channels postsynaptically with receptors above 

-

Basal ganglia, cerebellum, hippocampus, somatosensory cortex

Principal neurons

 

Reaction kinetics for the different reaction steps

-

Basal ganglia, cerebellum, hippocampus, somatosensory cortex

Principal neurons

 

Dose-dependent ligand-activation properties

-

Basal ganglia, cerebellum, hippocampus, somatosensory cortex

Principal neurons

 

Calcium dynamics measurements from spines and dendrites

 

-

Basal ganglia, cerebellum, hippocampus, somatosensory cortex

Principal neurons

 

Validation data in the form of: 

Activation profiles of target proteins when combinations of receptors are activated (data used for model building)

-

Basal ganglia, cerebellum, hippocampus, somatosensory cortex

Principal neurons

 

Validation data in the form of: 

Time courses of phosphorylation and dephosphorylation of target molecules when e.g. combinations of receptors are activated (if not used for model building)

-

Basal ganglia, cerebellum, hippocampus, somatosensory cortex

Principal neurons

 

 

Contact: Andrei Kramer, KTH Royal Institute of Technology, Sweden

 

Inhibition and Ca2+ Cascades

Type of data

Species

Brain region

Cell type

Calcium dynamics in dendritic compartments

Mouse/Rat

Cortex

Neurons

Electrophysiology and plasticity measurements

Mouse/Rat

Cortex

Pyramidal neurons

Morphometry of spines and dendritic arbor

Mouse/Rat

Cortex

Pyramidal neurons

Set of properties of receptors (GABA, NMDA, AMPA, mGluR5, CB1)

Mouse/Rat

General

Neurons

Set of properties of plasticity-related molecules (Cam, CaMKII, PKC, PKA, G-proteins and others)

Mouse/Rat

General

Neurons

Reaction kinetics for interactions between plasticity-related molecules

Mouse/Rat

General

Neurons

 

Contact: Antoine Triller and Pablo Serna, École Normale Supérieure, Paris, France

 

Molecular Models

Model of Ligand Dissociation Mechanism in M2 Muscarinic Receptor (with/without Allosteric Ligand)

Type of data

Species

Brain region

Cell type

New structural data of ligands bound to M2 receptor

-

-

-

Training or validation data in the form of ligand dissociation rate constants or residence times

-

-

-

 

Molecular Model of G Protein Regulation of Adenylyl Cyclase

Type of data

Species

Brain region

Cell type

New structural data of G proteins bound to adenylyl cyclase

-

-

-

Dissociation rate contants or binding affinities for the molecular species involved

-

-

-

Vaidation data in the form of association rate constants for the molecular species involved

-

-

-

 

Contact: Daria Kokh, Heidelberg Institute for Theoretical Studies, Germany

 

Multiscale

Multiscale Models of Calcium- and G-Protein Dependent Cascades (e.g. Endocannabinoid) in Single Cell Striatal Medium Spiny Neuron (Electrophysiological Model)

Type of data

Species

Brain region

Cell type

Striatal neuron model with enhanced calcium dynamics

Mouse

Striatum

Striatal projection neuron from the direct and indirect pathways

Detailed spines from a principal neuron

Mouse

Striatum

Striatal projection neuron from the direct and indirect pathways

Measurements of calcium in spines and dendrites of principal neurons

Mouse

Striatum

Striatal projection neuron from the direct and indirect pathways

 

Contact: Jeanette Hellgren Kotaleski, KTH Royal Institute of Technology, Sweden

 

Basal Ganglia

Striatal Scaffold Network (Unit Volume)

Type of data

Species

Brain region

Cell type

Microcircuit Level – Reconstruction

 

 

 

Architecture

 

 

 

Cell densities and density distribution

Mouse

Basal ganglia (striatum)

Projection neurons, interneurons

Micro-connectomics data for corticostriatal and thalamostriatal and Globus Pallidus Externa 

Mouse/Rat

Basal ganglia (striatum, pallidum)

Projection neurons, interneurons

Cellular Anatomy

 

 

 

Reconstructions of cells (dendrites + axons)

Mouse

Basal ganglia (striatum)

Projection neurons, interneurons

Single Cell Level - Reconstruction

 

 

 

Density of axon collaterals

Mouse

Basal ganglia (striatum)

Projection neurons, interneurons

Distribution of dendritic spines

Mouse

Basal ganglia (striatum)

Projection neurons, LTS interneurons

Single Cell Biophysics - Components

 

 

 

Genetic expression of ion channels (single-cell RNA-seq)

Mouse

Basal ganglia

All

Ion channel kinetics

Mouse

Basal ganglia

Projection neurons, interneurons

Distribution of ion channels

Mouse

Basal ganglia (striatum)

Projection neurons, interneurons

Postsynaptic currents (short-term plasticity) for corticostriatal, thalamostriatal and pallidal projections

Mouse

Basal ganglia (striatum)

Projection neurons, interneurons

 

Contact: Alexander Kozlov, Karolinska Institute, Sweden

 

Cerebellum

Cerebellum Scaffold Network

Type of data

Species

Brain region

Cell type

Microcircuit Level – Reconstruction

 

 

 

Architecture

 

 

 

Cells densities (accurate neuronal cell populations count and density estimation)

Mouse/Rat

Cerebellum

All

Cells positioning (from atlases)

Mouse/Rat

Cerebellum

All

Connectivity ratios

Mouse/Rat

Cerebellum

All

In vitro and in vivo data at the mesoscale level

Mouse/Rat

Cerebellum

All

 

 

 

 

Cellular anatomy

 

 

 

Reconstructions of cells (dendrites + axons)

Mouse/Rat

Cerebellum

All

 

 

 

 

Single Cell Level - Reconstruction

 

 

 

Morphologically detailed light-microscopic (or equivalent) 3D reconstruction of a neuron

Mouse/Rat/Human

Cerebellum

Purkinje, Deep cerebellar nuclei, Inferior olive, Lugaro cells

 

 

 

 

Single Cell Biophysics Components

 

 

 

Passive biophysical properties

Mouse/Rat

Cerebellum

Stellate and basket cells, Lugaro cells

Ion channel classes and kinetics:

Potassium chloride-dependent

TRPC, TRPM, TRPV channels

Mouse/Rat

Cerebellum

 All

Ion channel distribution

Mouse/Rat

Cerebellum

Stellate and basket cells, Deep cerebellar nuclei

Synaptic inputs:

MgluR1 – 5

5HT

Mouse/Rat

Cerebellum 

All

 

 

 

 

Single Cell Electrophysiology

 

 

 

Somatic recordings to (standardised) stimulus

Mouse/Rat

Cerebellum

Lugaro cells

Dendritic recordings to (standardised) stimulus

Mouse/Rat

Cerebellum

All

Axonal recordings to (standardised) stimulus

Mouse/Rat

Cerebellum

All

 

 

 

 

Single Cell Level - Validation

Mouse/Rat

Cerebellum

All

 

Contact: Simona Tritto and Elisa Marenzi, Università degli studi di Pavia, Italy

 

Hippocampus

Hippocampus CA1 Scaffold Network

Type of data

Species

Brain region

Cell type

Microcircuit Level - Reconstruction

 

 

 

Architecture

 

 

 

Overall neuronal cell counts/densities

Rat

Hippocampus (CA1)

Pyramidal cells, interneurons

Cell counts/densities/ratios for specific cell types

Rat

Hippocampus (CA1)

Pyramidal cells, interneurons

 

 

 

 

Cellular anatomy

 

 

 

3D reconstructions of cells (dendrites + axons) with 3D location

Rat

Hippocampus (CA1)

Pyramidal cells, interneurons

 

 

 

 

Synaptic properties

 

 

 

Paired electrophysiological recordings

Rat

Hippocampus (CA1)

Pyramidal cells, interneurons

Recordings with pathway stimulation

Rat

Hippocampus (CA1)

Pyramidal cells, interneurons

 

 

 

 

Microcircuit Level - Validation

 

 

 

Architecture

 

 

 

Gene expression maps

Rat

Hippocampus (CA1)

Pyramidal cells, interneurons

Tissue staining for cell-type-specific proteins

Rat

Hippocampus (CA1)

Pyramidal cells, interneurons

 

 

 

 

Synaptic properties

 

 

 

Connectivity ratios

Rat

Hippocampus (CA1)

Pyramidal cells, interneurons

Bouton density and number of synapses per connection

Rat

Hippocampus (CA1)

Pyramidal cells, interneurons

Divergence and convergence data

Rat

Hippocampus (CA1)

Pyramidal cells, interneurons

 

 

 

 

Network dynamics

 

 

 

Firing rate during spontaneous network activity (in vitro and in vivo)

Rat

Hippocampus (CA1)

Pyramidal cells, interneurons

LFP recordings of spontaneous/evoked activity

Rat

Hippocampus (CA1)

Pyramidal cells, interneurons

Extracellular multielectrode recordings of spontaneous/evoked activity

Rat

Hippocampus (CA1)

Pyramidal cells, interneurons

Changes in LFP/spiking in response to changes in extracellular ionic composition

Rat

Hippocampus (CA1)

Pyramidal cells, interneurons

Changes in LFP / spiking in response to pharmacological manipulations

Rat

Hippocampus (CA1)

Pyramidal cells, interneurons

 

Contact: Armando Romani, École Polytechnique Fédérale de Lausanne, Switzerland

Mouse Cells

Type of data

Species

Brain region

Cell type

Single Cell Level - Reconstruction

 

 

 

Morphologically detailed light-microscopic (or equivalent) 3D reconstruction of a neuron

Mouse

Hippocampus (CA1, CA3, DG)

 

All

 

 

 

 

Single cell biophysics components

 

 

 

Passive biophysical properties

Mouse

Hippocampus (CA1, CA3, DG)

All

Ion channels classes and kinetics

Mouse

Hippocampus (CA1, CA3, DG)

All

Subcellular ion channel distribution

Mouse

Hippocampus (CA1, CA3, DG)

All

Synaptic inputs

Mouse

Hippocampus (CA1, CA3, DG)

All

 

 

 

 

Single cell electrophysiology

 

 

 

Somatic recordings to (standardised) stimulus

Mouse

Hippocampus (CA1, CA3, DG)

All

 

 

 

 

Single Cell Level - Validation

 

 

 

Electrical neuron model properties

 

 

 

Somatic voltage responses to various current injection protocols

Mouse

Hippocampus (CA1, CA3, DG)

All

EPSP attenuation

Mouse

Hippocampus (CA1, CA3, DG)

All

Ephys changes under varying ionic compositions

Mouse

Hippocampus (CA1, CA3, DG)

All

Ephys changes with ion channel blockers

Mouse

Hippocampus (CA1, CA3, DG)

All

Calcium imaging data

Mouse

Hippocampus (CA1, CA3, DG)

All

Dendritic voltage recordings

Mouse

Hippocampus (CA1, CA3, DG)

All

Response to glutamate uncaging

Mouse

Hippocampus (CA1, CA3, DG)

All

 

Contact: Szabolcs Káli, Institute of Experimental Medicine, Hungarian Academy of Sciences

 

Somatosensory Cortex

Somatosensory Cortex Scaffold Network

Type of data

Species

Brain region

Cell type

Microcircuit Level - Reconstruction

 

 

 

Architecture

 

 

 

Overall neuronal cell counts/densities

Mouse

Somatosensory Cortex

Pyramidal cells, interneurons

Cell counts/densities/ratios for specific cell types

Mouse

Somatosensory Cortex

Pyramidal cells, interneurons

 

 

 

 

Cellular anatomy

 

 

 

3D reconstructions of cells (dendrites + axons) with 3D location

Mouse

Somatosensory Cortex

Pyramidal cells, interneurons

 

 

 

 

Synaptic properties

 

 

 

Paired electrophysiological recordings

Mouse

Somatosensory Cortex

Pyramidal cells, interneurons

Recordings with pathway stimulation

Mouse

Somatosensory Cortex

Pyramidal cells, interneurons

 

 

 

 

Microcircuit Level - Validation

 

 

 

Architecture

 

 

 

Gene expression maps

Mouse

Somatosensory Cortex

Pyramidal cells, interneurons

Tissue staining for cell-type-specific proteins

Mouse

Somatosensory Cortex

Pyramidal cells, interneurons

 

 

 

 

Synaptic properties

 

 

 

Connectivity ratios

Mouse

Somatosensory Cortex

Pyramidal cells, interneurons

Bouton density and number of synapses per connection

Mouse

Somatosensory Cortex

Pyramidal cells, interneurons

Divergence and convergence data

Mouse

Somatosensory Cortex

Pyramidal cells, interneurons

 

 

 

 

Network dynamics

 

 

 

Firing rate during spontaneous network activity (in vitro and in vivo)

Mouse

Somatosensory Cortex

Pyramidal cells, interneurons

LFP recordings of spontaneous/evoked activity

Mouse

Somatosensory Cortex

Pyramidal cells, interneurons

Extracellular multielectrode recordings of spontaneous/evoked activity

Mouse

Somatosensory Cortex

Pyramidal cells, interneurons

Changes in LFP/spiking in response to changes in extracellular ionic composition

Mouse

Somatosensory Cortex

Pyramidal cells, interneurons

Changes in LFP/spiking in response to pharmacological manipulations

Mouse

Somatosensory Cortex

Pyramidal cells, interneurons

 

Contact: Vishal Sood and Eilif Muller, École Polytechnique Fédérale de Lausanne, Switzerland

 

Whole Mouse Brain

Whole Mouse Brain (v1.0)

Type of data

Species

Brain region

Cell type

Simplified version of the detailed microcircuit of the CA1 hippocampus

Mouse

Hippocampus

-

Simplified version of the detailed microcircuit of the somatosensory cortex

Mouse

Cortex

-

Region-specific cell-type distribution 

Mouse

Any (e.g. hypothalamus)

Any (e.g. pyramidal cell)

Cell-type (M-Type) to electrical-type (E-type) distribution 

Mouse

Any 

Any

Point neuron parameters (with corresponding E-type) 

Mouse

Any

Any

M-type/E-type to M-type/E-type connection types 

Mouse

Any

Any

Connection types to synaptic parameters

Mouse

Any

Any

 

Contact: Dimitri Rodarie, École Polytechnique Fédérale de Lausanne, Switzerland