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
Central Nervous System bioactive compounds
Central Nervous System (CNS) is a platform designed to efficiently generate and parameterize bioactive conformers of ligands binding to neuronal proteins. The project is part of the Parameter generation and mechanistic studies of neuronal cascades using multi-scale molecular simulations of the Human Brain Project. CNS conformers are generated using a powerful multilevel strategy that combines a low-level (LL) method for sampling the conformational minima and high-level (HL) ab-initio calculations for estimating their relative stability. CNS database presents the results in a graphical user interface, displaying small molecule properties, analyses and generated 3D conformers. All data produced by the project is available to download. CNS will contribute in the improvement of the understanding of neuronal signalling cascades by protein structure-based simulations, calculating thermodynamics and kinetics constants of the molecular processes.
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