NeuroML-DB: Sharing and characterizing data-driven neuroscience models described in NeuroML

• DOI: 10.1371/journal.pcbi.1010941
• Publication Date: 2023-03-03T18:34:45Z
• Authors: Justas Birgiolas; Vergil Haynes; Padraig Gleeson; Richard C. Gerkin; Suzanne W. Dietrich; Sharon Crook
• Keywords: Computational neuroscience; Systems neuroscience; Computational model; Neuroinformatics

As researchers develop computational models of neural systems with increasing sophistication and scale, it is often the case that fully de novo model development impractical inefficient. Thus arises a critical need to quickly find, evaluate, re-use, build upon components developed by other researchers. We introduce NeuroML Database (NeuroML-DB.org), which has been address this complement sharing resources. NeuroML-DB stores over 1,500 previously published ion channels, cells, networks have translated modular description language. The database also provides reciprocal links neuroscience databases (ModelDB, Open Source Brain) as well access original publications (PubMed). These along Neuroscience Information Framework (NIF) search functionality provide deep integration community modeling resources greatly facilitate task finding suitable for reuse. Serving an intermediate language, its tooling ecosystem enable efficient translation popular simulator formats. nature enables analysis large number inspection their properties. Search capabilities database, together web-based, programmable online interfaces, allow rapidly assess stored electrophysiology, morphology, complexity use these perform database-scale neuron channel describe novel tetrahedral structure formed cell clusters in space properties features. This further information about similarity enrich search.