Extension of NEURON simulator for simulation of reaction-diffusion in neurons

用于模拟神经元反应扩散的神经模拟器的扩展

基本信息

批准号：
10434955
负责人：
William W Lytton
金额：
$ 41.09万
依托单位：
SUNY DOWNSTATE MEDICAL CENTER
依托单位国家：
美国
项目类别：
财政年份：
2010
资助国家：
美国
起止时间：
2010-06-01 至 2026-04-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10434955
关键词：
3-Dimensional Adoption Alzheimer&apos s Disease Amyloid Bayesian Analysis Biological Biology Biomedical Engineering Blood Brain Brain Chemistry Brain Diseases Cells Chemical Agents Chemicals Clinical Communities Complement Complex Computational Biology Computers Dendrites Development Differential Equation Diffusion Disease Documentation Edema Education Educational process of instructing Educational workshop Electrophysiology (science)Epilepsy Equation Extracellular Space Failure Functional disorder Funding Future Gap Junctions Gatekeeping Genome Heart High Performance Computing Homeostasis Hormones Human Information Theory Intracellular Space Ischemia Kinetics Learning Link Manuals Medical Memory Mental disorders Modality Modeling Myocardial Infarction Nerve Nerve Degeneration Nerve Fibers Nervous system structure Neurologic Neurons Neurosciences Neurotransmitters Organ Oxygen Pathology Pattern Recognition Performance Persons Pharmaceutical Preparations Pharmacologic Substance Pharmacology Play Process Proteome Pythons Reaction Reading Recovery Research Research Personnel Rest Role Running Savings Second Messenger Systems Signal Transduction Speed Stroke Structure Synapses Synaptic Transmission Systems Biology Techniques Thinking Time Tissues Toxin Travel Trees Vertebral column Work application programming interface artificial neural network autism spectrum disorder base body system brain dysfunction brain research chemical reaction computational neuroscience computer science experimental study improved in vivo interoperability meetings multi-scale modeling neglect neocortical nervous system disorder neurotechnology novel online course online tutorial personalized medicine postsynaptic pressure presynaptic reconstruction relating to nervous system reuptake simulation syntax synuclein tau Proteins tool transcriptome

项目摘要

Development of simulation bioengineering techniques in medical neuroscience has been limited due to computational neuroscience's focus on the higher capacities of humans, such as the ability to play chess or go. That has led to the notion that the brain can best be understood by recourse to the concepts of computer science: artificial neural networks, information theory, Bayesian inference, pattern recognition, etc. Whether or not these tools are sufficient for understanding human neocortical function, they are clearly not sufficient for understanding the nervous system dysfunction seen in neurological and psychiatric pathology. Brain disease, like diseases of other organ systems, is disease of biological tissue, and must eventually consider energetics and oxygenation, blood and brain pressures, as well as chemical reactions and diffusion of toxins and pharmaceuticals. Such full-organ simulation will require linkages to other simulators. Through such linkages, as well as through internal extensions, we have been extending the widely-used NEURON simulator to handle reaction-diffusion in neural tissue in order to better understand brain signaling, neurodegenerative toxic cascades, and drug effects. For the current funding period we will further augment NEURON's NRxD module through 4 Aims: 1. Improve synaptic modeling techniques by considering presynaptic volume, cleft and postsynaptic volume together to handle ionotropic synapses, metabotropic synapses, gap junctions and complex combination synapses; along with reuptake, diffusion, electrodiffusion, neurotransmitters, second messengers and retrograde neurotransmitters in a coordinated way. 2. Allow more rapid and more extensive exploration of parameter space by improving simulation speed and by allowing full state variable saving for improved simulation initialization and recovery from high-performance computing failures. 3. Develop both Python-based and socket-based application programming interfaces (APIs) for easier linkage with other simulators, including for electrodiffusion and for various types of stochastic simulation. 4. Continue package dissemination and education in order to get more computational and experimental NRxD users. We will continue to offer twice-yearly tutorials, and to sponsor additional workshops at Computational Neuroscience and at other meetings. We will integrate online tutorials with the documentation to provide both Programmer's Reference and Biological Reference online manuals. We will develop a set of video tutorials associated with these that will eventually be linked together to make an online course. Overall, we expect that our novel simulation neurotechnology will be of increasing use and utilization both for research use, and for future clinical adoption in personalized medicine.

由于计算神经科学的重点是人类的较高能力，例如玩耍的能力国际象棋或去。这导致了这样的观念，即大脑可以通过求助于计算机科学的概念：人工神经网络，信息理论，贝叶斯推论，模式识别等。这些工具是否足以理解人类新皮质功能，它们显然不足以理解神经系统在神经和精神病病理学中可见的功能障碍。脑疾病，例如其他疾病器官系统是生物组织疾病，最终必须考虑能量学和氧合，血液和大脑压力以及化学反应以及毒素和扩散药品。这样的全器仿真将需要与其他模拟器链接。通过这种连接以及通过内部扩展，我们一直在扩展广泛使用的神经元模拟器处理神经组织中的反应扩散以更好地了解大脑信号传导，神经退行性毒性级联反应和药物作用。在当前的资金期内我们将通过4个目标进一步增强神经元的NRXD模块：1。改进突触建模技术通过考虑突触前体积，裂口和突触后体积一起处理离子旋转突触，代谢突触，间隙连接和复杂的组合突触；以及重新摄取，扩散，电泄殖当，神经递质，第二使者和逆行神经递质以一种协调的方式。 2。允许对参数空间通过提高模拟速度并允许全州变量节省从高性能计算失败中改进了模拟初始化和恢复。 3。开发基于Python和基于插座的应用程序编程接口（API），以便于与其他模拟器的链接，包括用于电泄殖和各种随机的链接模拟。 4。继续包装传播和教育，以获得更多的计算和实验性NRXD用户。我们将继续提供每年两次的教程，并为赞助商提供计算神经科学和其他会议上的其他研讨会。我们将在线整合文档的教程可提供程序员的参考和生物参考在线手册。我们将开发与这些相关的一组视频教程，最终将链接在一起以进行在线课程。总体而言，我们希望我们的新颖模拟神经技术的使用和利用都将在研究用途和将来越来越多个性化医学的临床采用。