计算神经科学
计算神经科学是使用数学分析和计算机模拟的方法在不同水平上对神经系统进行模拟和研究： 从神经元的真实生物物理模型，它们的动态交互关系以及神经网络的学习， 到脑的组织和神经类型计算的量化理论等，从计算角度理解脑，研究非程序的、 适应性的、大脑风格的信息处理的本质和能力，探索新型的信息处理机理和途径， 从而创造脑。它的发展将对智能科学、信息科学、认知科学、神经科学等产生重要影响。
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计算神经科学
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GitHub上有人整合的计算神经科学资源
链接：open-computational-neuroscience-resources
以下为摘录的一部分感兴趣的内容：
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Open Courses
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- Computational Neuroscience at Coursera
- Computational Neuroscience: Neuronal Dynamics of Cognition at edX
- Neuronal Dynamics at edX
- Neuroscience course material from OpenCourseWare (OCW) at MIT Department of Brain and Cognitive Sciences - HUGE list!
- Simulation Neuroscience at edX
- Interactive webpage illustrating spiking neural models
- A series of notebooks that serves as an introduction to theoretical/computational neuroscience (for beginners)
- Introduction To Modern Brain-Computer Interface Design
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Open Data
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- This only lists neuroscience-specific open data repositories. For general science data repositories that may contain neuroscience data like re3data, see this Open Science Resources page
- 3D Brain Atlas Reconstructor
- Allen Brain Atlas Data Portal
- BODB - Brain Operation Database System
- BossDB.org — hundreds of terabytes of microscopy
- Brain Slices- Repository of brain tissue images
- C-BIG - Biological Imaging and Genetic repository
- Channelpedia - Wiki of neuron ion channels, hosted by the Blue Brain Project
- CRCNS - Collaborative Research in Computational Neuroscience
- GIN - Modern Research Data Management for Neuroscience
- IDA LONI - Image and Data Archive for neuroscience by Laboratory of Neuro Imaging
- INDI - International Neuroimaging Data-Sharing Initiative
- iEEG.org - National Institutes of Neurological Disorders and Stroke EEG data repository for epilepsy research
- NCBI databases - National Center for Biotechnology Information database list, VERY comprehensive!
- NDA - National Institute of Mental Health Data Archive
- NeuroVault - Public repository of MRI and PET statistical maps, parcellations, and atlases
- NIF - Neuroscience Information Framework, massive search engine for neuroscience data, tools, etc.
- NITRC - NeuroImaging Tools and Resources Collaboratory
- NMC - Neocortical Microcircuit Collaboration, part of Blue Brain
- NWB - Neurodata Without Borders - A standardized format for electrophysiological, and in the future other, neuroscience data. Some data sets available on the site in this format.
- OpenNeuro - Free and open platform for neuroimaging data (succeeds OpenfMRI)
- Whole Brain Catalog - Virtual catalog of a mouse brain
- WormBase - Database of nematode information
- ZFIN - Zebrafish Model Organism Database
Open Data Schema
- Neo - Python library for enabling interoperability of electrophysiological data, including conversion from proprietary file formats
- Neurodata Without Borders: Neurophysiology (NWB:N) data standard for neurophysiology, including intracellular, extracellular, optical physiology, tracking, and stimulus data
- NSDF - Neuroscience Simulation Data Format, built on top of HDF5
- SONATA format for large-scale, efficient model specification and output data schema of neural simulations, co-developed by Allen Institute for Brain Sciences and Blue Brain Project
Open Model Repositories
- BioModels - Not neuroscience-specific
- ModelDB - Repository of computational neuroscience models for simulation, built by Senselab
- Senselab hosts several other databases, but ModelDB is the most popular:
- CellPropDB - Cellular Properties Database provides a simple repository for data regarding membrane channels, receptor and neurotransmitters that are expressed in specific types of cells.
- NeuronDB - Provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances.
- MicrocircuitDB - Provides an accessible location for storing and efficiently retrieving realistic computational models of brain microcircuits and networks.
- 3DModelDB - A collection of 3D printable versions of published neuron morphologies, both traced and artificial.
- ORModelDB - A resource that is a repository of the results of the efforts of the community is computationally elucidating the structure of the olfactory receptor with a view to establishing a mechanistic basis for OR-odorant binding.
- OdorMapDB - Olfactory Bulb Odor Map DataBase
- OdorDB - Odor Molecules DataBase
- ORDB - Olfactory Receptor DataBase
- NeuroElectro - Repository of data-mined and human-curated neuron celltype electrophysiological data
- NeuroMorpho - Curated repository of digitally reconstructed neuron geometries
- OSB - Open Source Brain
- OpenWorm - Popular platform for simulation and analysis of nematode neuroscience models!
- "Integrated Models" RRID on SciCrunch - Compilation of model sources
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Open Code
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Based on Imaging Analysis
- Allen SDK - Allen (Institute) Software Development Kit for Allen Brain Atlas
- CaImAn - Calcium Imaging Analysis
- CATMAID - The Collaborative Annotation Toolkit for Massive Amounts of Image Data
- FreeSurfer - Popular open-source MRI processing and analysis software
- NiBabel - Python library for enabling interoperability of neuroimaging data, including conversion from and between many file formats
- TrakEM2 - Morphological data mining and analysis tool
- TREES - MATLAB toolbox for analyzing neuron microscopy
- V-NeuroStack - 3D time stacks for finding patterns in spontaneous activity of neurons in mouse brain slices
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Organizations and Communities
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- CodeNeuro - Bringing neuroscience and data science together
- CNS - Organization for Computational Neuroscience
- G-NODE - German Informatics Node
- INCF - International Neuroinformatics Coordinating Facility
- NeuralEnsemble, focused on software development in neuroscience
- Neuroinformatics Research Group at Harvard
- Neurostars - Neuroscience Q and A website
- NIMH - National Institute of Mental Health
- An Open Computational Neuroscience list I've made on Twitter
- Organization for Human Brain Mapping
- Reddit /r/Neuroscience resources
- SFN - Society for Neuroscience
计算神经科学在线课程
1. 计算神经科学系列课程
苏黎世大学与苏黎世联邦理工大学共建的转化神经模型单元（Translational Neuromodeling Unit，简称TNU）的系列教学视频，包括计算精神病学（含视频、幻灯片、代码等），计算神经影像诊断，以及fMRI数据分析方法与模型等。
2. 计算神经科学（Rajesh P. N. Rao & Adrienne Fairhall）
英文名Computational Neuroscience，是Coursera上的华盛顿大学的计算神经科学基本参考《理论神经科学》来上，比较全面。
3. 纽约大学 - 神经与认知科学的数学工具（Mike Landy & Eero Simoncelli）
Mathematical Tools for Neural and Cognitive Science，这是纽约大学的研究生课程，让学生学习神经和认知数据和系统的可视化、分析和建模的基本数学方法。本课程涵盖数学和统计工具的基本集合，提供假设、动机、逻辑和几何直觉，以及每个工具的简单推导。概念通过大量的计算练习得到加强。目标是让学生能够理解、使用和解释这些工具。有视频（zoom中国区看不到），课件和作业。
4. 计算神经科学导论（麻省理工学院，Sebastian Seung，2004）
5. 计算神经科学：认知的神经动力学（洛桑联邦理工学院，edX）
6. 神经信息学（伦敦大学学院，Kenneth Harris & Matteo Carandini）
其它数据
| ADNI dataset | IDA |
| ATLASES | |