The Cellullar Level Simulation Interactive Workflows and Use Cases guide the users through the resolution of realistic scientific problems. They are implemented as either front-end or full stack web applications or Python based Jupyter Notebooks that allow to interactively build, reconstruct or simulate data-driven brain models and perform data analysis visualization. Web applications are freely accessible and only require authentication to EBRAINS when specific actions are required (e.g., submitting a simulation job to an HBP HPC system). Jupyter Notebooks are cloned to the lab.ebrains.eu platform and requires authentication via an EBRAINS account. If you do not have an account yet, please sign up (an institutional email address is required).

NeuroFeatureExtract

Extracts electrophysiological features; traces can be from HBP/EBRAINS or uploaded
Credits: Luca Leonardo Bologna (lucaleonardo.bologna@cnr.it); Roberto Smiriglia (roberto.smiriglia@ibf.cnr.it); Dario Curreri (dario.curreri@ibf.cnr.it)

Hodgkin-Huxley Neuron Builder

Use the eFEL and BluePyOpt libraries to go through the entire neuron builder pipeline: 1) feature extraction, 2) model optimization, 3) simulation.

Credits: Luca Leonardo Bologna (lucaleonardo.bologna@cnr.it); Roberto Smiriglia (roberto.smiriglia@ibf.cnr.it)

Mouse O1 - Scaffold Somatosensory Cortex Microcircuit for Mouse

This model combines specific datasets obtained for mouse somatosensory cortex, models of neuronal electrophysiology constrained to mouse primary visual cortex data from the Allen Cell Types Database, and datasets that were algorithmically transformed from rat to mouse.

Credits: Michael W. Reimann (michael.reimann@epfl.ch)Eilif Muller (eilif.mueller@epfl.ch)Srikanth Ramaswamy (srikanth.ramaswamy@epfl.ch)

Rat hippocampus CA1

A circuit of detailed neuron models based on the Ascoli atlas.

Credits: Szabolcs Káli (kali@koki.hu); Audrey Mercer (a.mercer@ucl.ac.uk); Michele Migliore (michele.migliore@yale.edu); Armando Romani (armando.romani@epfl.ch); Eilif Muller (eilif.mueller@epfl.ch)

Multiscale brain circuit models of M1 and CA3

Large-scale and biologically realistic models of rodent motor (M1) thalamocortical circuits and a model of CA3 microcircuits showing cross-frequency coupling. Models were developed using the NetPyNE multiscale modeling tool.

Credits: Salvador Dura-Bernal (salvador.dura-bernal@downstate.edu); Joe Graham (joe.w.graham@gmail.com); Eugenio Urdapilleta (urdapile@gmail.com); Joao Moreira (joao.moreira@downstate.edu)William Lytton (bill.lytton@downstate.edu)Samuel Neymotin (samuel.neymotin@nki.rfmh.org)