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, 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