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The TVB pipeline allows neuroscientists to automatically extract structural connectomes from diffusion-weighted MRI data and functional connectomes from fMRI data based on a number of state-of-the-art methods for image processing, tractography reconstruction and connectome generation. Pipeline output can be directly uploaded to The Virtual Brain neuroinformatics platform for large-scale brain simulation. Further pipeline outputs include: raw tractography output (track streamlines), structural (coupling weights and distances) and functional connectomes, region-wise fMRI time series, M/EEG region-wise source activity time series. The pipeline supports the following atlasses: AAL, AAL2, Craddock200, Craddock400, Desikan Killiany, Destrieux, Human Connectome Project Multimodal Parcellation and Perry512.

The pipeline is available as a Docker container based on the BIDS MRtrix3 App containing environment and software for connectome extraction (e.g. FreeSurfer, FSL, MRtrix). The container makes use of parallelized software that can be run with multiple threads locally or on supercomputers. Input data must be provided in BIDS format. As a minimum, dwMRI and strucutral MRI scans need to be provided. In addition, the pipeline can process fMRI (region-wise fMRI time courses and functional connectomes), EEG and MEG data (region-wise source activity time courses).

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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