A MATLAB® toolbox that given a three-dimensional spine reconstruction computes a set of characteristic morphological measures that unequivocally determine the spine shape.
Toolkit for mathematical simulations of signal-transduction pathway models of G-protein coupled receptors.
The SSB Toolkit is a Python library specifically designed for conducting simulations of mathematical models that represent the signal-transduction pathways of G-protein coupled receptors (GPCRs). This library consists of a set of systems biology simulation routines, enabling the investigation of pharmacodynamic models associated with GPCRs. It provides a means to explore how the structural characteristics of these receptors influence subcellular signaling dynamics.
Other softwareAll software
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.
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.