Computational

Computational neuroscience data encompasses neuronal models, morphological reconstructions, and the simulation code and environments used to produce, test, and reproduce them. This perspective covers the format standards, specialised archives, and collaborative platforms that constitute the open computational neuroscience ecosystem.

Standards

NeuroML is the simulator-independent XML-based language for describing data-driven models of neurons and networks at multiple levels of biological detail. It is endorsed by INCF and supported by conversion tools for NEURON, NEST, MATLAB, and other simulation environments, enabling models described in NeuroML to be run on any compliant simulator. SWC is the standard interchange format for three-dimensional neuronal morphology reconstructions, storing branching structure as a sequence of cylindrical compartments with spatial coordinates. SWC is endorsed by INCF and is the mandatory format for all reconstructions archived in NeuroMorpho.Org.

Archives

ModelDB is the primary open repository for published computational neuroscience models, operated by Yale University since 1996. Researchers deposit the simulation code associated with a published paper, enabling others to verify, reproduce, and extend the model. Code can be submitted in any simulation language, with strong support for NeuroML format. NeuroMorpho.Org is the open archive for digitally reconstructed neuron and glia morphologies from across species, standardising all reconstructions in SWC format and providing a programmatic API for retrieval. Morphologies from NeuroMorpho.Org are widely used as the anatomical substrate for biophysically detailed models in ModelDB and OpenSourceBrain.

Simulation environments and platforms

OpenSourceBrain (OSB) is a web platform for sharing and collaboratively developing standardised computational models of neurons and circuits. Unlike traditional model databases that archive frozen publication snapshots, OSB hosts models that evolve collaboratively over time. It uses NeuroML as its primary format and provides browser-based 3D visualisation and simulation through OSBv1. OSBv2 extends this scope to integrate experimental data from DANDI Archive directly alongside models, with cloud-based workspaces supporting NetPyNE for network model development and NWB Explorer for NWB-formatted experimental data exploration.

For the citation, licensing, and long-term preservation practices that make computational models FAIR research outputs, see Reproducibility. For the experimental electrophysiology and imaging data used to constrain and validate computational models, see Electrophysiology and Neuroimaging.