Ecosystem

Arbor exists in a wider computational neuroscience software ecosystem. The Arbor simulator is also not the only component written by the Arbor developers.

Arbor software

Arbor

The Arbor simulator.

modcc

An important component of Arbor. It is the compiler for the Arbor dialect of NMODL, a language commonly used to describe mechanisms on morphologically detailed cable cells. modcc does not have its own documentation; the best resource is the file format page describing it NMODL.

NSuite

A framework for maintaining and running benchmarks and validation tests for multi-compartment neural network simulations on HPC systems. NSuite documentation

Arbor GUI

The Arbor GUI visualizes cable cells and can be used to decorate morphologies. Single cell simulations can be ran (using the Arbor simulator) and output plotted right from the GUI. Code repository and Readme

nmlcc

Arbor has built-in read support for NeuroML morphologies, but not yet for other NeuroML components (mechanisms, networks). nmlcc is compiler/translator that aims to generate complete Arbor inputs for any NeuroML file. Code repository and Readme

../_images/arbor.png

Arbor tools in relationship to each other and common file formats. Red outlines indicate currently unplanned format format support (figure generated from arbor.dot).

Wider ecosystem

Simulators

Arbor exists in the wider computational neuroscience simulator ecosystem. Simulators exist roughly at these four levels: ranging from the lowest level (molecular dynamics) to the highest (whole brain simulation). Needless to say, each level comes with a higher level of abstraction, but attempt to describe larger structures. Co-simulation or Multiscale simulations refers to the attempt to link up the levels and simulators in an attempt to combine the low level of detail (in regions where it is desired) with the effects of the larger structures. The concrete method to interface between levels are typically the submission of spikes, ion (concentrations), field potentials.

Neural Mass Models
The Virtual Brain
Point Neurons
NEST
BRIAN
Detailed Neurons
Arbor
(Core)NEURON, NeuroGPU
GENESIS
MOOSE
LEMS
jNML
EDEN
Molecular Dynamics
ALMOST
NAMD
An informal hierarchy of the simulator landscape, showing Arbor's position.

Frameworks

Certain tools combine various components to create integrated experimentation toolchains. They do not only include (interfaces for) simulators, but also converters for file formats, miscellaneous data processing (pre or post), plotting, miscellaneous analysis, and more. An incomplete list: