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:9893029
- 负责人:
- 金额:$ 40.8万
- 依托单位:
- 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 2021-06-30
- 项目状态:已结题
- 来源:
- 关键词:3-DimensionalAlgorithmsAlzheimer&aposs DiseaseApicalAreaAstrocytesBiochemicalBrainBrain DiseasesCell membraneCellsCellular biologyChemicalsClinicCodeCommunitiesComplementComplexComputer SimulationComputersCytosolDendritesDevelopmentDifferential EquationDiffusionDiseaseDocumentationEducational workshopElectrophysiology (science)EnvironmentFundingGenomicsLanguageLawsLearningLinkLocationMemoryMental disordersMethodsMindModelingMolecularMolecular BiologyMonte Carlo MethodMosaicismNatureNerveNerve FibersNeurobiologyNeuronsOrganOrganellesPerformancePharmacotherapyProteomicsPythonsReactionResourcesRunningSchizophreniaSecond Messenger SystemsSignal TransductionSpeedStochastic ProcessesSystemSystems BiologyTechniquesTechnologyTimeTrainingTranslational ResearchTravelVariantautism spectrum disordercell typechemical reactioncomputational neurosciencedata miningdesigngraphical user interfacehigh end computerimprovedinformation processingknowledge basemodel designmodel developmentmulti-scale modelingmulticore processorneglectnervous system disorderopen sourceparallelizationphenomenological modelsprogramspublic health relevancerelating to nervous systemsimulationsimulation environmenttoolvoltage
项目摘要
DESCRIPTION (provided by applicant): Multiscale modeling using computer simulation is increasingly recognized as a major method, along with data-mining, for assimilating the vast and ever-growing knowledge base in systems biology. This will improve understanding of the links between molecules and disease manifestation for translational research to the clinic. The bridging of chemophysiology (chemical signaling in neurons and astrocytes) with electrophysiology provides a fundamental connection that will necessarily underpin higher organizational scales. Multiscale models are particularly difficult to simulate in neurobiology du to the elongated nature of neural cells (compared to compact cells for many other cell types), and to multiple overlapping of embedded scales (e.g., pyramidal apical dendrite domains at the same temporal and spatial scale as local networks). We are developing the widely used NEURON simulator to accommodate simulation of these complex second-messenger signal interactions that contribute to information processing. In the prior funding period, we added the reaction-diffusion module to NEURON, providing 3D deterministic diffusion linked to reactions situated in cytosol, on or within internal organelles, or on plasma membrane. We also added 1D deterministic diffusion to reduce high computational loads that limited the scope of simulations, noting that the detail of full 3D diffusion is not always needed. As part of these improvements, we extended NEURON's Python interface to include a new set of classes devoted to reaction-diffusion modeling. Additionally, we prepared connectors for interfacing with SBML (Systems Biology Markup Language). In the current proposal, we will build on these advances in order to allow development of "mosaic" simulations involving combinations of stochastic and deterministic simulation in both 3D and 1D. This will involve the ability to readily switch among these different levels of approximation so that different modeling approaches can be compared. These objectives will be achieved through the following Specific Aims: Aim 1. Multiple multigrid methods: 1D and 3D grids with different sized grids at different locations. Aim 2. Parallelization using multisplit methods that allow the simulation of a single neuron to be run across multiple processors or across multiple threads on a single processor. Aim 3. Stochastic simulation using an extended Gillespie method. This will complement additional stochastic methods that will also be made available in NEURON. Aim 4. Dissemination: new Graphical User Interface for front-end specifications for viewing results, model development, model importation and merging, method comparison and multiprocessor deployment. Making the tool accessible to the community via courses, tutorials, example programs, documentation and online help.
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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William W Lytton其他文献
Multiscale modeling of cortical information flow in Parkinson's disease
- DOI:
10.1186/1471-2202-14-s1-o21 - 发表时间:
2013-07-08 - 期刊:
- 影响因子:2.300
- 作者:
Cliff C Kerr;Sacha J van Albada;Samuel A Neymotin;George L Chadderdon III;Peter A Robinson;William W Lytton - 通讯作者:
William W Lytton
Transformation of inputs in a model of the rat hippocampal CA1 network
- DOI:
10.1186/1471-2202-11-s1-p56 - 发表时间:
2010-07-20 - 期刊:
- 影响因子:2.300
- 作者:
Andrey V Olypher;William W Lytton;Astrid A Prinz - 通讯作者:
Astrid A Prinz
Ih modulates theta rhythm and synchrony in computer model of CA3
- DOI:
10.1186/1471-2202-13-s1-p80 - 发表时间:
2012-07-16 - 期刊:
- 影响因子:2.300
- 作者:
Markus M Hilscher;Thiago Moulin;Yosef Skolnick;William W Lytton;Samuel A Neymotin - 通讯作者:
Samuel A Neymotin
Interlaminar Granger causality and alpha oscillations in a model of macaque cortex
- DOI:
10.1186/1471-2202-12-s1-p208 - 发表时间:
2011-07-18 - 期刊:
- 影响因子:2.300
- 作者:
Cliff C Kerr;Jue Mo;Samuel Neymotin;Mingzhou Ding;William W Lytton - 通讯作者:
William W Lytton
Parallelizing large networks using NEURON-Python
- DOI:
10.1186/1471-2202-16-s1-p151 - 发表时间:
2015-12-18 - 期刊:
- 影响因子:2.300
- 作者:
Alexandra H Seidenstein;Robert A McDougal;Michael L Hines;William W Lytton - 通讯作者:
William W Lytton
William W Lytton的其他文献
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{{ truncateString('William W Lytton', 18)}}的其他基金
Microconnectomics of neocortex: a multiscale computer model
新皮质微连接组学:多尺度计算机模型
- 批准号:
8926428 - 财政年份:2014
- 资助金额:
$ 40.8万 - 项目类别:
Microconnectomics of neocortex: a multiscale computer model
新皮质微连接组学:多尺度计算机模型
- 批准号:
8743695 - 财政年份:2014
- 资助金额:
$ 40.8万 - 项目类别:
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
- 批准号:
10434955 - 财政年份:2010
- 资助金额:
$ 40.8万 - 项目类别:
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
- 批准号:
10615791 - 财政年份:2010
- 资助金额:
$ 40.8万 - 项目类别:
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
- 批准号:
10299041 - 财政年份:2010
- 资助金额:
$ 40.8万 - 项目类别:
THALAMOCORTICAL NEURON DYNAMICS AND ABSENCE EPILEPSY
丘脑皮质神经元动力学与失神性癫痫
- 批准号:
2270191 - 财政年份:1993
- 资助金额:
$ 40.8万 - 项目类别:
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