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
Ginkgo/MEDUSA
Ginkgo/MEDUSA (Microstructure Environment Designer Using Sphere Atoms) is a HPC compatible simulation tool that allows an all-in one simulation of brain tissue microstructure and their diffusion MRI signal relying on 3 simulation features:
- Simulation of realistic geometries representing cell membranes populating brain gray and white matters to create virtual tissues using a generative approach called MEDUSA,
- Simulation of the diffusion process of water molecules present within tissues using a Monte-Carlo approach,
- Simulation of the attenuation of the diffusion MRI signal for any tuning of a diffusion-weighted MRI pulse sequence (Pulsed Gradient Spin Echo, Oscillating Gradient Spin Echo, Abritrary Gradient Spin Echo, ….).
The Ginkgo/MEDUSA tool is dedicated to the development of computational models of brain tissue microstructure in order to go beyond existing analytical models known to be limited to accurately represent the complexity of brain cellular environments
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