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

描述（由申请人提供）：计算系统生物学的多尺度建模对于神经科学以及生物医学研究的其他领域越来越重要。 在神经元和神经元网络的背景下，整合最近的研究结果在计算细胞生物学和突触功能，将需要模拟，可以将反应扩散建模到基因组和蛋白质组表达的水平。 这将允许模拟发生在细胞体、树突和棘中的复杂的生化相互作用。 为此，设计用于模拟电生理学的NEURON模拟器需要进行重大扩展。 主要扩展将涉及在现有的多室电压积分基础上增加三维细胞内空间积分和配准。 前端和后端的额外扩展也将需要使新工具完全可用。 这项工作将与康涅狄格大学健康中心的VCell团队合作完成，他们将为我们提供集成程序的代码，并将为这些复杂模拟所需的其他查看器的开发提供咨询。 该程序还将确保与VCell模拟器、其他现有的可读写SBML（系统生物学标记语言）和NeuroML的细胞生物学模拟器的互操作性。 NEURON的扩展将通过以下具体目标实现。 1. 从其他动态标记语言的动态翻译。 2. 三维细胞内反应扩散模型的实现。 3. 开发两个主要驱动项目：A。 ALS相关的线粒体转运功能障碍的模型; B. 模型的化学通量之间的脊柱和树突。 4. 传播新工具。 传播对于确保650多名活跃的NEURON用户中的一些人使用新工具至关重要。 我们还将努力鼓励细胞神经生物学家将NEURON和VCell纳入他们的技术库。 这两个主要平台之间的模型的准备翻译，使用数百同行评审公布的模拟可用，将鼓励模拟重用和新的应用程序的速度开发。

DESCRIPTION (provided by applicant): Multiscale modeling for computational systems biology is growing in importance for neuroscience as well as for other areas of biomedical research. Integration of recent findings in computational cell biology and synapse function, in the context of neurons and neuronal networks, will require simulations that can incorporate reaction-diffusion modeling down to the level of genomic and proteomic expression. This will allow simulation of the complex biochemical interactions occurring in cell bodies, dendrites and spines. To do this, the NEURON simulator, designed to simulate electrophysiology, will require major extensions. The primary extension will involve addition of 3-dimensional intracellular spatial integration with registration to the existing multicompartment voltage integration. Additional extensions at front and back- ends will also be needed to make the new tools fully useable. This work will be done in collaboration with the VCell team at University of Connecticut Health Center, who will provide us with code from their integration procedures and will consult on development of additional viewers that will be needed for these complex simulations. This procedure will also ensure interoperability with the VCell simulator, other existing cell biology simulators that read and write SBML (Systems Biology markup-language), and NeuroML. The extensions to NEURON will be effected through the following Specific Aims. 1. Kinetic translation from other kinetic markup languages. 2. Implementation of 3-D intracellular reaction diffusion modeling. 3. Development of two primary driving projects: a. model of ALS-related mitochondrial transport dysfunction; b. model of chemical fluxes between spine and dendrite. 4. Dissemination of the new tools. Dissemination is of critical importance to ensure that the new tool is used by some of the more than 650 active NEURON users. We will also make efforts to encourage cell neurobiologists to incorporate both NEURON and VCell into their technique repertoire. The ready translation of models between these two major platforms, using the several hundred peer-review published simulations available, will encourage simulation reuse and speed development of new applications.