3DSpineMFE
A MATLAB® toolbox that given a three-dimensional spine reconstruction computes a set of characteristic morphological measures that unequivocally determine the spine shape.
Modelling and simulation
Interactive Workflows for Cellular Level Modeling
Build, reconstruct, and simulate data-driven brain models
- 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
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.
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.
Get in contact with the Interactive Workflows and Use Cases team and user community
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.
Other software
All softwareArbor
Arbor is a high-performance library for computational neuroscience simulations with multi-compartment, morphologically-detailed cells, from single cell models to very large networks. Arbor is written from the ground up with many-cpu and gpu architectures in mind, to help neuroscientists effectively use contemporary and future HPC systems to meet their simulation needs. Arbor supports NVIDIA and AMD GPUs as well as explicit vectorization on CPUs from Intel (AVX, AVX2 and AVX512) and ARM (Neon and SVE). When coupled with low memory overheads, this makes Arbor an order of magnitude faster than the most widely-used comparable simulation software. Arbor is open source and openly developed, and we use development practices such as unit testing, continuous integration, and validation.
Modelling and simulationCellular level simulation
BioExcel Building Blocks
BioExcel Building Blocks Workflows is a collection of biomolecular workflows to explore the flexibility and dynamics of macromolecules, including signal transduction proteins or molecules related to the Central Nervous System. Molecular dynamics setup for protein and protein-ligand complexes are examples of workflows available as Jupyter Notebooks. The workflows are built using the BioBB software library, developed in the framework of the BioExcel Centre of Excellence. BioBBis a collection of Python wrappers on top of popular biomolecular simulation tools, offering a layer of interoperability between the wrapped tools, which make them compatible and prepared to be directly interconnected to build complex biomolecular workflows.
Modelling and simulationMolecular and subcellular simulation