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
NetPyNE GUI
The UI splits the workflows in two tabs available at the top of the screen: define your network and create network.
The NetPyNE GUI is implemented on top of Geppetto,
an open-source platform that provides the infrastructure for building tools for visualizing neuroscience models and data and for managing simulations in a highly accessible way.
The GUI is defined using JavaScript, React and HTML5. This offers a flexible and intuitive way to create advanced layouts while still enabling each of the elements of the interface to be synchronized with the Python model. The interactive
Python backend is implemented as a Jupyter Notebook extension which provides direct communication with the Python kernel. This makes it possible to synchronize the data model underlying the GUI with a custom Python-based NetPyNE model. This functionality is at the heart of the GUI and means any change made to the NetPyNE model in the Python kernel is immediately reflected in the GUI and vice versa. The tool’s GUI is available at https://github.com/Neurosim-lab/NetPyNE-UI and is under active development.
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