开源网络工具时代的亮点
Highlights from the Era of Open Source Web-Based Tools.
机构信息
Departments of Pediatrics and Psychiatry, Columbia University, New York, New York 10032.
Division of Developmental Psychobiology, New York State Psychiatric Institute, New York, New York 10032.
出版信息
J Neurosci. 2021 Feb 3;41(5):927-936. doi: 10.1523/JNEUROSCI.1657-20.2020. Epub 2021 Jan 20.
Abstract
High digital connectivity and a focus on reproducibility are contributing to an open science revolution in neuroscience. Repositories and platforms have emerged across the whole spectrum of subdisciplines, paving the way for a paradigm shift in the way we share, analyze, and reuse vast amounts of data collected across many laboratories. Here, we describe how open access web-based tools are changing the landscape and culture of neuroscience, highlighting six free resources that span subdisciplines from behavior to whole-brain mapping, circuits, neurons, and gene variants.
摘要
高数字连接性和对可重复性的关注正在推动神经科学领域的开放科学革命。存储库和平台已经出现在各个子学科领域，为我们在分享、分析和重用来自许多实验室收集的大量数据的方式上带来了范式转变。在这里，我们描述了开放获取的基于网络的工具如何改变神经科学的格局和文化，重点介绍了跨越从行为到全脑映射、电路、神经元和基因变体等子学科的六个免费资源。
相似文献
1
Highlights from the Era of Open Source Web-Based Tools.开源网络工具时代的亮点
J Neurosci. 2021 Feb 3;41(5):927-936. doi: 10.1523/JNEUROSCI.1657-20.2020. Epub 2021 Jan 20.
2
Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits.开放源脑：可视化、分析、模拟和开发神经元和电路标准化模型的协作资源。
Neuron. 2019 Aug 7;103(3):395-411.e5. doi: 10.1016/j.neuron.2019.05.019. Epub 2019 Jun 11.
3
A unified platform to manage, share, and archive morphological and functional data in insect neuroscience.一个用于管理、共享和存档昆虫神经科学形态学和功能数据的统一平台。
Elife. 2021 Aug 24;10:e65376. doi: 10.7554/eLife.65376.
4
New approaches to neural circuits in behavior.行为的神经回路新方法。
Learn Mem. 2012 Aug 16;19(9):385-90. doi: 10.1101/lm.025049.111.
5
Imaging zebrafish neural circuitry from whole brain to synapse.从全脑到突触对斑马鱼神经回路进行成像。
Front Neural Circuits. 2013 Apr 24;7:76. doi: 10.3389/fncir.2013.00076. eCollection 2013.
6
Brain Networks and Cognitive Architectures.脑网络与认知结构
Neuron. 2015 Oct 7;88(1):207-19. doi: 10.1016/j.neuron.2015.09.027.
7
Uncovering the Transcriptional Correlates of Hub Connectivity in Neural Networks.揭示神经网络中枢纽连接的转录相关性。
Front Neural Circuits. 2019 Jul 19;13:47. doi: 10.3389/fncir.2019.00047. eCollection 2019.
8
[In vivo visualization of functional neural circuits].[功能性神经回路的体内可视化]
Tanpakushitsu Kakusan Koso. 2008 Mar;53(4 Suppl):525-30.
9
Establishment and Maintenance of Neural Circuit Architecture.建立和维护神经回路结构。
J Neurosci. 2021 Feb 10;41(6):1119-1129. doi: 10.1523/JNEUROSCI.1143-20.2020.
10
Cracking neural circuits in a tiny brain: new approaches for understanding the neural circuitry of Drosophila.破解微小大脑中的神经回路：理解果蝇神经回路的新方法
Trends Neurosci. 2008 Oct;31(10):512-20. doi: 10.1016/j.tins.2008.07.006. Epub 2008 Sep 3.
引用本文的文献
1
Genetic modulation of protein expression in rat brain.大鼠脑中蛋白质表达的基因调控
iScience. 2025 Feb 21;28(3):112079. doi: 10.1016/j.isci.2025.112079. eCollection 2025 Mar 21.
2
Innovations in noninvasive sensory stimulation treatments to combat Alzheimer's disease.用于对抗阿尔茨海默病的非侵入性感觉刺激疗法的创新。
PLoS Biol. 2025 Feb 28;23(2):e3003046. doi: 10.1371/journal.pbio.3003046. eCollection 2025 Feb.
3
A localized tracing technique to explore intra-amygdala functional and structural correlates of individual variability in behavioral response.一种局部追踪技术，用于探索杏仁核内与行为反应个体差异相关的功能和结构关联。
Front Mol Neurosci. 2025 Jan 22;18:1347539. doi: 10.3389/fnmol.2025.1347539. eCollection 2025.
4
Accelerating the continuous community sharing of digital neuromorphology data.加速数字神经形态学数据的持续社区共享。
FASEB Bioadv. 2024 Jun 17;6(7):207-221. doi: 10.1096/fba.2024-00048. eCollection 2024 Jul.
5
Automatic identification of scientific publications describing digital reconstructions of neural morphology.自动识别描述神经形态数字重建的科学出版物。
Brain Inform. 2023 Sep 8;10(1):23. doi: 10.1186/s40708-023-00202-x.
6
A guide to the BRAIN Initiative Cell Census Network data ecosystem.《脑计划细胞普查网络数据生态系统指南》
PLoS Biol. 2023 Jun 30;21(6):e3002133. doi: 10.1371/journal.pbio.3002133. eCollection 2023 Jun.
7
Automatic identification of scientific publications describing digital reconstructions of neural morphology.自动识别描述神经形态数字重建的科学出版物。
bioRxiv. 2023 Feb 15:2023.02.14.527522. doi: 10.1101/2023.02.14.527522.
8
Assisted neuroscience knowledge extraction via machine learning applied to neural reconstruction metadata on NeuroMorpho.Org.通过应用于NeuroMorpho.Org上神经重建元数据的机器学习辅助神经科学知识提取。
Brain Inform. 2022 Nov 7;9(1):26. doi: 10.1186/s40708-022-00174-4.
9
Cell morphologies in the nervous system: Glia steal the limelight.神经系统中的细胞形态：神经胶质细胞抢尽风头。
J Comp Neurol. 2023 Feb;531(3):338-343. doi: 10.1002/cne.25429. Epub 2022 Oct 31.
10
Large scale similarity search across digital reconstructions of neural morphology.大规模跨数字重建神经形态相似性搜索。
Neurosci Res. 2022 Aug;181:39-45. doi: 10.1016/j.neures.2022.05.004. Epub 2022 May 14.
本文引用的文献
1
A manifesto for reproducible science.可重复科学宣言。
Nat Hum Behav. 2017 Jan 10;1(1):0021. doi: 10.1038/s41562-016-0021.
2
A Comparison of Dopaminergic and Cholinergic Populations Reveals Unique Contributions of VTA Dopamine Neurons to Short-Term Memory.多巴胺能和胆碱能群体的比较揭示了 VTA 多巴胺神经元对短期记忆的独特贡献。
Cell Rep. 2020 Dec 15;33(11):108492. doi: 10.1016/j.celrep.2020.108492.
3
Regional, Layer, and Cell-Type-Specific Connectivity of the Mouse Default Mode Network.区域、层和细胞类型特异性连接的小鼠默认模式网络。
Neuron. 2021 Feb 3;109(3):545-559.e8. doi: 10.1016/j.neuron.2020.11.011. Epub 2020 Dec 7.
4
BRICseq Bridges Brain-wide Interregional Connectivity to Neural Activity and Gene Expression in Single Animals.BRICseq 将全脑区域间连通性与单个动物的神经活动和基因表达联系起来。
Cell. 2020 Jul 9;182(1):177-188.e27. doi: 10.1016/j.cell.2020.05.029. Epub 2020 Jul 2.
5
Reproducibility of animal research in light of biological variation.鉴于生物学变异性，动物研究的可重复性。
Nat Rev Neurosci. 2020 Jul;21(7):384-393. doi: 10.1038/s41583-020-0313-3. Epub 2020 Jun 2.
6
The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas.艾伦鼠脑通用坐标系：一个 3D 参考图谱。
Cell. 2020 May 14;181(4):936-953.e20. doi: 10.1016/j.cell.2020.04.007. Epub 2020 May 7.
7
An open-source framework for neuroscience metadata management applied to digital reconstructions of neuronal morphology.一种用于神经科学元数据管理的开源框架，应用于神经元形态的数字重建。
Brain Inform. 2020 Mar 26;7(1):2. doi: 10.1186/s40708-020-00103-3.
8
Module for SWC neuron morphology file validation and correction enabled for high throughput batch processing.SWC 神经元形态文件验证和校正模块，支持高通量批处理。
PLoS One. 2020 Jan 23;15(1):e0228091. doi: 10.1371/journal.pone.0228091. eCollection 2020.
9
Cerebral cortical folding, parcellation, and connectivity in humans, nonhuman primates, and mice.人类、非人灵长类动物和小鼠的大脑皮质折叠、分区及连接
Proc Natl Acad Sci U S A. 2019 Dec 26;116(52):26173-26180. doi: 10.1073/pnas.1902299116. Epub 2019 Dec 23.
10
Individual structural features constrain the mouse functional connectome.个体结构特征限制了小鼠的功能连接组。
Proc Natl Acad Sci U S A. 2019 Dec 26;116(52):26961-26969. doi: 10.1073/pnas.1906694116. Epub 2019 Dec 11.
Zotero 插件