Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

State Space Representation01:27

State Space Representation

469
The frequency-domain technique, commonly used in analyzing and designing feedback control systems, is effective for linear, time-invariant systems. However, it falls short when dealing with nonlinear, time-varying, and multiple-input multiple-output systems. The time-domain or state-space approach addresses these limitations by utilizing state variables to construct simultaneous, first-order differential equations, known as state equations, for an nth-order system.
Consider an RLC circuit, a...
469
Model Approaches for Pharmacokinetic Data: Distributed Parameter Models01:06

Model Approaches for Pharmacokinetic Data: Distributed Parameter Models

205
Pharmacokinetic models are mathematical constructs that represent and predict the time course of drug concentrations in the body, providing meaningful pharmacokinetic parameters. These models are categorized into compartment, physiological, and distributed parameter models.
The distributed parameter models are specifically designed to account for variations and differences in some drug classes. This model is particularly useful for assessing regional concentrations of anticancer or...
205
Protein Networks02:26

Protein Networks

2.7K
2.7K
Protein Networks02:26

Protein Networks

4.4K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.4K
Multicompartment Models: Overview01:14

Multicompartment Models: Overview

445
Multicompartment models are mathematical constructs that depict how drugs are distributed and eliminated within the body. They segment the body into several compartments, symbolizing various physiological or anatomical areas connected through drug transfer processes such as absorption, metabolism, distribution, and elimination.
These models offer a more comprehensive representation of drug behavior in the body than one-compartment models. They accommodate the complexity of drug distribution,...
445
2D NMR: Overview of Homonuclear Correlation Techniques01:16

2D NMR: Overview of Homonuclear Correlation Techniques

559
Homonuclear correlation spectroscopy (COSY) is a powerful technique used in Nuclear Magnetic Resonance (NMR) spectroscopy to study the correlations between nuclei of the same type within a molecule. It provides information about scalar couplings between adjacent nuclei, which helps determine connectivity and structural information. There are several COSY variants, each with its unique strengths and experimental parameters.
COSY90 is the standard two-dimensional (2D) COSY experiment that...
559

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Neurosift: DANDI exploration and NWB visualization in the browser.

Journal of open source software·2026
Same author

NeuroConv: Streamlining Neurophysiology Data Conversion to the NWB Standard.

Proceedings of the Python in Science Conferences. Python in Science Conference·2026
Same author

Deep-learning-assisted simulation of a cortical circuit: integrating anatomy, physiology and function.

bioRxiv : the preprint server for biology·2026
Same author

Neuronal silence as a predictive biomarker and target for epileptic seizures suppression.

Scientific reports·2026
Same author

Modeling and simulation of neocortical micro- and mesocircuitry (Part I, anatomy).

eLife·2026
Same author

Modeling and simulation of neocortical micro- and mesocircuitry (Part II, Physiology and experimentation).

eLife·2026

Related Experiment Video

Updated: Dec 27, 2025

Modeling the Functional Network for Spatial Navigation in the Human Brain
05:55

Modeling the Functional Network for Spatial Navigation in the Human Brain

Published on: October 13, 2023

1.4K

The SONATA data format for efficient description of large-scale network models.

Kael Dai1, Juan Hernando2, Yazan N Billeh1

  • 1Allen Institute for Brain Science, Seattle, Washington, United States of America.

Plos Computational Biology
|February 25, 2020
PubMed
Summary
This summary is machine-generated.

A new data format, Scalable Open Network Architecture TemplAte (SONATA), enables efficient building, simulation, and sharing of complex computational neuroscience models. This open-source format enhances reproducibility and scalability for large-scale neural circuit research.

More Related Videos

Statistical Modelling of Cortical Connectivity Using Non-invasive Electroencephalograms
08:51

Statistical Modelling of Cortical Connectivity Using Non-invasive Electroencephalograms

Published on: November 1, 2019

6.0K
Author Spotlight: Advancing Large-Scale Neural Dynamics Through HD-MEA Technology
09:44

Author Spotlight: Advancing Large-Scale Neural Dynamics Through HD-MEA Technology

Published on: March 8, 2024

5.6K

Related Experiment Videos

Last Updated: Dec 27, 2025

Modeling the Functional Network for Spatial Navigation in the Human Brain
05:55

Modeling the Functional Network for Spatial Navigation in the Human Brain

Published on: October 13, 2023

1.4K
Statistical Modelling of Cortical Connectivity Using Non-invasive Electroencephalograms
08:51

Statistical Modelling of Cortical Connectivity Using Non-invasive Electroencephalograms

Published on: November 1, 2019

6.0K
Author Spotlight: Advancing Large-Scale Neural Dynamics Through HD-MEA Technology
09:44

Author Spotlight: Advancing Large-Scale Neural Dynamics Through HD-MEA Technology

Published on: March 8, 2024

5.6K

Area of Science:

  • Computational Neuroscience
  • Neuroscience Data Standards

Background:

  • Computational neuroscience models are growing in scale and complexity.
  • High-performance computing and large datasets necessitate efficient data formats.

Purpose of the Study:

  • To develop a flexible, high-performance data format for large-scale neuroscience models.
  • To support model construction, simulation, and data sharing.

Main Methods:

  • Development of the Scalable Open Network Architecture TemplAte (SONATA) data format.
  • Standardized file representation for neuronal circuits and simulation data.
  • Provision of reference Application Programming Interfaces (APIs) and model examples.

Main Results:

  • SONATA is designed for memory and computational efficiency across platforms.
  • The format allows flexibility for extensions and new conventions.
  • SONATA is integrated into multiple modeling and visualization tools.

Conclusions:

  • SONATA addresses the need for a broadly applicable data format in computational neuroscience.
  • The open-source format promotes efficient model building, sharing, and reproducibility.
  • SONATA aims to catalyze community adoption and advance large-scale neural modeling.