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
Extrae
Extrae is a dynamic instrumentation package to trace programs compiled and run with the shared memory model (like OpenMP and pthreads), the message passing (MPI) programming model or both programming models (different MPI processes using OpenMP or pthreads within each MPI process). Instrumentation of CUDA, CUPTI, OpenCL, Python multiprocessing, Java threads and relevant system, dynamic memory and I/O calls is also supported. Extrae generates trace files that can be visualized with Paraver.
Extrae is currently available on different architectures and operating systems, including: GNU/Linux (x86, x86_64, ARM, POWER), IBM AIX, SGI Altix, Open Solaris, FreeBSD, Android, Fujitsu FX10/100, Cray XT, IBM Blue Gene, Intel Xeon Phi, GPUs and FPGAs.
The combined use of Extrae and Paraver offers an enormous analysis potential, both qualitative and quantitative. With these tools the actual performance bottlenecks of parallel applications can be identified. The microscopic view of the program behavior that the tools provide is very useful to optimize the parallel program performance.
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