NESTML: a generic modeling language and code generation tool for the simulation of spiking neural networks with advanced plasticity rules.

IF 2.5 4区 医学 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY
Frontiers in Neuroinformatics Pub Date : 2025-06-04 eCollection Date: 2025-01-01 DOI:10.3389/fninf.2025.1544143
Charl Linssen, Pooja N Babu, Jochen M Eppler, Luca Koll, Bernhard Rumpe, Abigail Morrison
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引用次数: 0

Abstract

With increasing model complexity, models are typically re-used and evolved rather than starting from scratch. There is also a growing challenge in ensuring that these models can seamlessly work across various simulation backends and hardware platforms. This underscores the need to ensure that models are easily findable, accessible, interoperable, and reusable-adhering to the FAIR principles. NESTML addresses these requirements by providing a domain-specific language for describing neuron and synapse models that covers a wide range of neuroscientific use cases. The language is supported by a code generation toolchain that automatically generates low-level simulation code for a given target platform (for example, C++ code targeting NEST Simulator). Code generation allows an accessible and easy-to-use language syntax to be combined with good runtime simulation performance and scalability. With an intuitive and highly generic language, combined with the generation of efficient, optimized simulation code supporting large-scale simulations, it opens up neuronal network model development and simulation as a research tool to a much wider community. While originally developed in the context of NEST Simulator, NESTML has been extended to target other simulation platforms, such as the SpiNNaker neuromorphic hardware platform. The processing toolchain is written in Python and is lightweight and easily customizable, making it easy to add support for new simulation platforms.

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一种通用的建模语言和代码生成工具,用于模拟具有高级可塑性规则的峰值神经网络。
随着模型复杂性的增加,模型通常被重用和发展,而不是从头开始。在确保这些模型能够无缝地跨各种仿真后端和硬件平台工作方面,也面临着越来越大的挑战。这强调了确保模型容易找到、可访问、可互操作和可重用的必要性——遵循FAIR原则。通过提供一种领域特定的语言来描述神经元和突触模型,NESTML解决了这些需求,这些模型涵盖了广泛的神经科学用例。该语言由代码生成工具链支持,该工具链自动为给定的目标平台生成低级模拟代码(例如,针对NEST模拟器的c++代码)。代码生成允许可访问且易于使用的语言语法与良好的运行时模拟性能和可伸缩性相结合。凭借直观和高度通用的语言,结合生成高效,优化的仿真代码,支持大规模仿真,它将神经网络模型开发和仿真作为一种研究工具开放给更广泛的社区。虽然最初是在NEST模拟器的背景下开发的,但NESTML已经扩展到针对其他仿真平台,例如SpiNNaker神经形态硬件平台。处理工具链是用Python编写的,轻量级且易于定制,因此可以轻松添加对新仿真平台的支持。
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来源期刊
Frontiers in Neuroinformatics
Frontiers in Neuroinformatics MATHEMATICAL & COMPUTATIONAL BIOLOGY-NEUROSCIENCES
CiteScore
4.80
自引率
5.70%
发文量
132
审稿时长
14 weeks
期刊介绍: Frontiers in Neuroinformatics publishes rigorously peer-reviewed research on the development and implementation of numerical/computational models and analytical tools used to share, integrate and analyze experimental data and advance theories of the nervous system functions. Specialty Chief Editors Jan G. Bjaalie at the University of Oslo and Sean L. Hill at the École Polytechnique Fédérale de Lausanne are supported by an outstanding Editorial Board of international experts. This multidisciplinary open-access journal is at the forefront of disseminating and communicating scientific knowledge and impactful discoveries to researchers, academics and the public worldwide. Neuroscience is being propelled into the information age as the volume of information explodes, demanding organization and synthesis. Novel synthesis approaches are opening up a new dimension for the exploration of the components of brain elements and systems and the vast number of variables that underlie their functions. Neural data is highly heterogeneous with complex inter-relations across multiple levels, driving the need for innovative organizing and synthesizing approaches from genes to cognition, and covering a range of species and disease states. Frontiers in Neuroinformatics therefore welcomes submissions on existing neuroscience databases, development of data and knowledge bases for all levels of neuroscience, applications and technologies that can facilitate data sharing (interoperability, formats, terminologies, and ontologies), and novel tools for data acquisition, analyses, visualization, and dissemination of nervous system data. Our journal welcomes submissions on new tools (software and hardware) that support brain modeling, and the merging of neuroscience databases with brain models used for simulation and visualization.
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