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NeuroML-DB: Sharing and characterizing data-driven neuroscience models described in NeuroML
Justas Birgiolas1, Vergil Haynes2,3, Padraig Gleeson4
1Ronin Institute, Montclair, New Jersey, United States of America.
Plos Computational Biology
|March 3, 2023
Summary
The NeuroML Database (NeuroML-DB.org) facilitates reusing computational neuroscience models. It stores over 1,500 models and links to other resources, enabling efficient model discovery and analysis.
Area of Science:
- Computational neuroscience
- Neuroscience informatics
- Bioinformatics
Background:
- Developing sophisticated computational models of neural systems is complex and time-consuming.
- A need exists for efficient methods to find, evaluate, and reuse existing models and model components.
Purpose of the Study:
- To introduce the NeuroML Database (NeuroML-DB.org) as a resource for sharing and reusing computational neuroscience models.
- To integrate with existing neuroscience databases and resources for enhanced model discovery.
Main Methods:
- Stored over 1,500 published models of ion channels, cells, and networks translated into the NeuroML language.
- Implemented reciprocal links to ModelDB, Open Source Brain, PubMed, and NIF search.
- Developed web-based and programmable interfaces for accessing model properties (electrophysiology, morphology, complexity).
Main Results:
- Established a database of over 1,500 NeuroML-formatted models.
- Facilitated deep integration with other neuroscience modeling resources.
- Enabled database-scale analysis, revealing a novel tetrahedral structure in cell model clusters.
Conclusions:
- The NeuroML Database enhances model reuse and discovery in computational neuroscience.
- The database's integration and analysis capabilities support efficient research and understanding of model properties.
