BAMS2工作区：一个用于整理和处理神经解剖连接的全面且通用的神经信息学平台。
BAMS2 workspace: a comprehensive and versatile neuroinformatic platform for collating and processing neuroanatomical connections.
作者信息
Bota Mihail, Talpalaru Stefan, Hintiryan Houri, Dong Hong-Wei, Swanson Larry W
机构信息
Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089.
出版信息
J Comp Neurol. 2014 Oct 1;522(14):3160-76. doi: 10.1002/cne.23592. Epub 2014 Apr 12.
Abstract
We describe a novel neuroinformatic platform, the BAMS2 Workspace (http://brancusi1.usc.edu), designed for storing and processing information on gray matter region axonal connections. This de novo constructed module allows registered users to collate their data directly by using a simple and versatile visual interface. It also allows construction and analysis of sets of connections associated with gray matter region nomenclatures from any designated species. The Workspace includes a set of tools allowing the display of data in matrix and networks formats and the uploading of processed information in visual, PDF, CSV, and Excel formats. Finally, the Workspace can be accessed anonymously by third-party systems to create individualized connectivity networks. All features of the BAMS2 Workspace are described in detail and are demonstrated with connectivity reports collated in BAMS and associated with the rat sensory-motor cortex, medial frontal cortex, and amygdalar regions.
相似文献
1
BAMS2 workspace: a comprehensive and versatile neuroinformatic platform for collating and processing neuroanatomical connections.BAMS2工作区：一个用于整理和处理神经解剖连接的全面且通用的神经信息学平台。
J Comp Neurol. 2014 Oct 1;522(14):3160-76. doi: 10.1002/cne.23592. Epub 2014 Apr 12.
2
Organizing principles for the cerebral cortex network of commissural and association connections.联络和联合连接的大脑皮层网络的组织原则。
Proc Natl Acad Sci U S A. 2017 Nov 7;114(45):E9692-E9701. doi: 10.1073/pnas.1712928114. Epub 2017 Oct 23.
3
Collating and Curating Neuroanatomical Nomenclatures: Principles and Use of the Brain Architecture Knowledge Management System (BAMS).整理和编纂神经解剖学术语：脑结构知识库（BAMS）的原则和应用。
Front Neuroinform. 2010 Mar 29;4:3. doi: 10.3389/fninf.2010.00003. eCollection 2010.
4
Cortical networks of the mouse brain elaborate within the gray matter.小鼠大脑的皮质网络在灰质内细化。
Brain Struct Funct. 2018 Nov;223(8):3633-3652. doi: 10.1007/s00429-018-1710-5. Epub 2018 Jul 9.
5
A new module for on-line manipulation and display of molecular information in the brain architecture management system.大脑结构管理系统中用于在线操作和显示分子信息的新模块。
Neuroinformatics. 2006 Winter;4(4):275-98. doi: 10.1385/NI:4:4:275.
6
Brain architecture management system.脑架构管理系统
Neuroinformatics. 2005;3(1):15-48. doi: 10.1385/NI:3:1:015.
7
Temporal Changes in Local Functional Connectivity Density Reflect the Temporal Variability of the Amplitude of Low Frequency Fluctuations in Gray Matter.局部功能连接密度的时间变化反映了灰质中低频波动幅度的时间变异性。
PLoS One. 2016 Apr 26;11(4):e0154407. doi: 10.1371/journal.pone.0154407. eCollection 2016.
8
Gray Matter and Functional Connectivity in Anterior Cingulate Cortex are Associated with the State of Mental Silence During Sahaja Yoga Meditation.在前扣带皮层中的灰质和功能连接与霎哈嘉瑜伽冥想中的精神静默状态有关。
Neuroscience. 2018 Feb 10;371:395-406. doi: 10.1016/j.neuroscience.2017.12.017. Epub 2017 Dec 22.
9
Topology of genetic associations between regional gray matter volume and intellectual ability: Evidence for a high capacity network.区域灰质体积与智力之间遗传关联的拓扑结构：高容量网络的证据。
Neuroimage. 2016 Jan 1;124(Pt A):1044-1053. doi: 10.1016/j.neuroimage.2015.09.046. Epub 2015 Sep 28.
10
Medial frontal white and gray matter contributions to general intelligence.内侧额叶白质和灰质对一般智力的贡献。
PLoS One. 2014 Dec 31;9(12):e112691. doi: 10.1371/journal.pone.0112691. eCollection 2014.
引用本文的文献
1
Brain-Wide Mapping of Axonal Connections: Workflow for Automated Detection and Spatial Analysis of Labeling in Microscopic Sections.轴突连接的全脑图谱：显微镜切片中标记的自动检测和空间分析工作流程
Front Neuroinform. 2016 Apr 19;10:11. doi: 10.3389/fninf.2016.00011. eCollection 2016.
2
The anatomical problem posed by brain complexity and size: a potential solution.大脑复杂性和大小所带来的解剖学问题：一个潜在的解决方案。
Front Neuroanat. 2015 Aug 20;9:104. doi: 10.3389/fnana.2015.00104. eCollection 2015.
3
Photonics meets connectomics: case of diffuse, long-range horizontal projections in rat cortex.光子学与连接组学的交汇：以大鼠皮层中的弥漫性、长程水平投射为例。
Neurophotonics. 2015 Oct;2(4):041403. doi: 10.1117/1.NPh.2.4.041403. Epub 2015 May 27.
4
Connections of the juxtaventromedial region of the lateral hypothalamic area in the male rat.雄性大鼠下丘脑外侧区近腹内侧区域的连接
Front Syst Neurosci. 2015 May 27;9:66. doi: 10.3389/fnsys.2015.00066. eCollection 2015.
5
Text mining for neuroanatomy using WhiteText with an updated corpus and a new web application.使用更新后的语料库和新的网络应用程序，通过WhiteText对神经解剖学进行文本挖掘。
Front Neuroinform. 2015 May 21;9:13. doi: 10.3389/fninf.2015.00013. eCollection 2015.
6
Ontology-based approach for in vivo human connectomics: the medial Brodmann area 6 case study.基于本体论的体内人类连接组学方法：内侧布罗德曼6区案例研究
Front Neuroinform. 2015 Apr 10;9:9. doi: 10.3389/fninf.2015.00009. eCollection 2015.
7
Architecture of the cerebral cortical association connectome underlying cognition.认知背后的大脑皮质联合连接组结构
Proc Natl Acad Sci U S A. 2015 Apr 21;112(16):E2093-101. doi: 10.1073/pnas.1504394112. Epub 2015 Apr 6.
本文引用的文献
1
Mapping brain circuitry with a light microscope.用光显微镜绘制大脑回路。
Nat Methods. 2013 Jun;10(6):515-23. doi: 10.1038/nmeth.2477.
2
Genetic approaches to neural circuits in the mouse.遗传方法研究小鼠的神经回路。
Annu Rev Neurosci. 2013 Jul 8;36:183-215. doi: 10.1146/annurev-neuro-062012-170307. Epub 2013 May 17.
3
CoCoMac 2.0 and the future of tract-tracing databases.CoCoMac 2.0 和轨迹追踪数据库的未来。
Front Neuroinform. 2012 Dec 27;6:30. doi: 10.3389/fninf.2012.00030. eCollection 2012.
4
A travel guide to Cytoscape plugins. Cytoscape 插件使用指南。
Nat Methods. 2012 Nov;9(11):1069-76. doi: 10.1038/nmeth.2212. Epub 2012 Nov 6.
5
Comprehensive connectivity of the mouse main olfactory bulb: analysis and online digital atlas.小鼠嗅球的全面连接：分析与在线数字图谱
Front Neuroanat. 2012 Aug 7;6:30. doi: 10.3389/fnana.2012.00030. eCollection 2012.
6
Neuroscience: Observatories of the mind.神经科学：心灵的观测站。
Nature. 2012 Mar 21;483(7390):397-8. doi: 10.1038/483397a.
7
Combining collation and annotation efforts toward completion of the rat and mouse connectomes in BAMS.在 BAMS 中，通过组合整理和注释工作来完成大鼠和小鼠连接组图谱。
Front Neuroinform. 2012 Feb 28;6:2. doi: 10.3389/fninf.2012.00002. eCollection 2012.
8
neuroVIISAS: approaching multiscale simulation of the rat connectome.神经 VIISAS：接近大鼠连接组的多尺度模拟。
Neuroinformatics. 2012 Jul;10(3):243-67. doi: 10.1007/s12021-012-9141-6.
9
The retrosplenial cortex: intrinsic connectivity and connections with the (para)hippocampal region in the rat. An interactive connectome.后隔核：大鼠内连接性及其与（副）海马区的连接。一个交互连接组。
Front Neuroinform. 2011 Jul 27;5:7. doi: 10.3389/fninf.2011.00007. eCollection 2011.
10
Projections of the medial orbital and ventral orbital cortex in the rat.大鼠眶内侧和眶腹侧皮质的投射。
J Comp Neurol. 2011 Dec 15;519(18):3766-801. doi: 10.1002/cne.22733.
Zotero 插件