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Multi-scale brain simulation with TVB-NEST

This Python package offers a convenient interface to set-up co-simulation models that simulate TVB large-scale brain network models that interact with NEST spiking neuron models.
NEST simulates neural activity at the microscopic spatial scale of single neurons or neuron networks. On the other hand, The Virtual brain simulates at the mesoscopic or macroscopic scales of large neural populations or brain regions. Here, both are brought together to enable neuroscientists to study how these different scales interact and how different scales inform activity "from the bottom up" and "down from the top".

A generic Python interface allows users to quickly and conveniently set up a parallel simulation in TVB and in NEST and automatically handles the exchange of currents, spikes, voltages, etc. between the different scales. Although the technical aspect of this tool is realized, the scientific part is a work in progress and we are continuously enriching the coupling between scales such that biophysical plausibility is maintained. The TVB+NEST bundle software package -- available as an easy-to-use Docker image container -- combines the sophistication and flexibility of NEST's spiking neuron simulation infrastructure with TVB's whole-brain simulation, processing, analyses and visualisation capabilities.

Other software

All software


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


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

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