The Interactive Workflows and Use Cases provide tools and services that enable you to work through a number of pipelines; these are categorized by level of expertise and by their service maturity level. Our community-driven work aims at involving as many scientists as possible. In order to reach this goal, results, methods and code are shared and made public to boost collaborative scientific advancements.
Interactive Workflows for Cellular Level Modeling
Build, reconstruct, and simulate data-driven brain models
Work through a number of pipelines for single cell model optimization of different brain region cells, run in silico experiments of individual neurons, small circuits and entire brain regions, perform ad hoc data analysis on electrophysiological data, synaptic events fitting, morphology analysis and visualization.
Our offer
- Build single cell, small circuit and brain area models
- Perform data analysis on recorded and simulated neural activity
- Run the models on EBRAINS HPC resources
- Share your results and code with the scientific community via the EBRAINS platforms
Tools
Reconstruct and simulate data-driven scaffold models of brain and brain tissue
The Workflows and Use Cases are implemented via web applications or Python based jupyter notebooks running on the EBRAINS jupyterlab platform. They allow to go through selected procedures related to a wide range of computational neuroscience applications; these includes: 1) extracting features from electrophysiological recordings or simulated neural activity; 2) building single cell hippocampal detailed NEURON models based on experimental data; 3) analyzing and visualizing reconstructed neural morphologies; 4) running in silico experiments on small circuits (built by the users from a reconstructed volume) and entire brain regions.
Depending on the Use Cases and Workflows, job submission to dedicated HPC systems might be required. Users can get access through their own credentials or through the service account utility, which we have specifically developed to lower access barrier for users less experienced in computational issues.
Most workflows require a free EBRAINS account.
