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用于虚拟神经元模型定义、网络配置、行为实验定义和实验结果可视化的基于网络的界面。

Web-Based Interfaces for Virtual Neuron Model Definition, Network Configuration, Behavioral Experiment Definition and Experiment Results Visualization.

作者信息

Epelde Gorka, Morgan Fearghal, Mujika Andoni, Callaly Frank, Leškovský Peter, McGinley Brian, Álvarez Roberto, Blau Axel, Krewer Finn

机构信息

Vicomtech, San Sebastián, Spain.

IIS Biodonostia, San Sebastián, Spain.

出版信息

Front Neuroinform. 2018 Nov 13;12:80. doi: 10.3389/fninf.2018.00080. eCollection 2018.

DOI:10.3389/fninf.2018.00080
PMID:30483089
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6243129/
Abstract

The platform targets the complete virtualization of the nematode , and its environment. This paper presents a suite of unified web-based Graphical User Interfaces (GUIs) as the main user interaction point, and discusses their underlying technologies and methods. The user-friendly features of this tool suite enable users to graphically create neuron and network models, and behavioral experiments, without requiring knowledge of domain-specific computer-science tools. The framework furthermore allows the graphical visualization of all simulation results using a worm locomotion and neural activity viewer. Models, experiment definitions and results can be exported in a machine-readable format, thereby facilitating reproducible and cross-platform execution of experiments in other simulation environments. This is made possible by a novel XML-based behavioral experiment definition encoding format, a NeuroML XML-based model generation and network configuration description language, and their associated GUIs. User survey data confirms the platform usability and functionality, and provides insights into future directions for web-based simulation GUIs of and other living organisms. The tool suite is available online to the scientific community and its source code has been made available.

摘要

该平台旨在实现线虫及其环境的完全虚拟化。本文介绍了一套基于网络的统一图形用户界面（GUI）作为主要用户交互点，并讨论了其底层技术和方法。该工具套件的用户友好特性使用户能够以图形方式创建神经元和网络模型以及行为实验，而无需具备特定领域计算机科学工具的知识。此外，该框架允许使用蠕虫运动和神经活动查看器对所有模拟结果进行图形化可视化。模型、实验定义和结果可以以机器可读格式导出，从而便于在其他模拟环境中进行可重复和跨平台的实验执行。这是通过一种新颖的基于XML的行为实验定义编码格式、一种基于NeuroML XML的模型生成和网络配置描述语言及其相关的GUI实现的。用户调查数据证实了该平台的可用性和功能，并为线虫及其他生物体基于网络的模拟GUI的未来发展方向提供了见解。该工具套件已在线向科学界提供，其源代码也已公开。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3b3/6243129/a70c9e43e443/fninf-12-00080-g0013.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3b3/6243129/98bd65da51f4/fninf-12-00080-g0001.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3b3/6243129/5d07a4cb5d57/fninf-12-00080-g0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3b3/6243129/d4eee27205b2/fninf-12-00080-g0007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3b3/6243129/af983b320b58/fninf-12-00080-g0008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3b3/6243129/8b3beaf2de98/fninf-12-00080-g0009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3b3/6243129/f3495be9fa1a/fninf-12-00080-g0010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3b3/6243129/728db4d94739/fninf-12-00080-g0011.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3b3/6243129/d7d9ab25ed30/fninf-12-00080-g0012.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3b3/6243129/a70c9e43e443/fninf-12-00080-g0013.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3b3/6243129/98bd65da51f4/fninf-12-00080-g0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3b3/6243129/85943066a427/fninf-12-00080-g0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3b3/6243129/bdaf0e03ff8f/fninf-12-00080-g0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3b3/6243129/438991869b5d/fninf-12-00080-g0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3b3/6243129/2d90fc922e2d/fninf-12-00080-g0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3b3/6243129/5d07a4cb5d57/fninf-12-00080-g0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3b3/6243129/d4eee27205b2/fninf-12-00080-g0007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3b3/6243129/af983b320b58/fninf-12-00080-g0008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3b3/6243129/8b3beaf2de98/fninf-12-00080-g0009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3b3/6243129/f3495be9fa1a/fninf-12-00080-g0010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3b3/6243129/728db4d94739/fninf-12-00080-g0011.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3b3/6243129/d7d9ab25ed30/fninf-12-00080-g0012.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3b3/6243129/a70c9e43e443/fninf-12-00080-g0013.jpg

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Modeling Behavioral Experiment Interaction and Environmental Stimuli for a Synthetic .为合成物模拟行为实验交互与环境刺激
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