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MSPViz is a web-based visualisation tool for structural plasticity models. It uses a novel visualisation technique based on the representation of neuronal information through the use of abstract levels and a set of representations in each level. This hierarchical representation lets the user interact and change the representation, modifying the degree of detail of the information to be analysed in a simple and intuitive way, through the navigation of different views at different levels of abstraction. The designed representations in each view only contain the necessary variables to achieve the desired tasks, thus avoiding overwhelming saturation of information. The multilevel structure and the design of the representations provide organised views, which facilitate visual analysis tasks. Moreover, each view has been enhanced adding line and bar charts to analyse trends in simulation data. Filtering and sorting capabilities can be applied on each view to ease the analysis. Additionally, some other views, such as connectivity matrices and force-directed layouts, have been incorporated, enriching the already existing views and improving the analysis process. Finally, this tool has been optimised to lower render and data loading times, even from remote sources such as WebDav servers.

Other software

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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

Arbor

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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