High Performance Computing for Multiscale Modeling of Biological Systems

用于生物系统多尺度建模的高性能计算

• 批准号: 8549842
• 负责人: Ivet Bahar
• 金额: $ 239.39万
• 依托单位: UNIVERSITY OF PITTSBURGH AT PITTSBURGH
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-09-24 至 2017-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8549842
• 关键词: Amino Acid Transporter; Area; Automobile Driving; Biological Sciences; Biomedical Technology; Brain; Cell model; Cells; Computational Biology; Disease; Excitatory Amino Acids; Goals; Health; High Performance Computing; Home environment; Image; Image Analysis; Institutes; Institution; Joints; Laboratories; Lead; Medical center; Modeling; Molecular; Molecular Models; Neurobiology; Neurons; Organism; Process; Proteins; Regulation; Research; Research Training; Services; Signal Transduction; Supercomputing; Synapses; System; Systems Biology; T-Lymphocyte; Technology; Tissues; Training; Transmission Electron Microscopy; Universities; Vertebral column; bioimaging; biological systems; calmodulin-dependent protein kinase II; computerized tools; dopamine transporter; insight; models and simulation; molecular modeling; multi-scale modeling; nervous system disorder; neurotransmitter transport; programs; reconstruction; relating to nervous system; research and development; structural biology; tool; trafficking; transmission process

DESCRIPTION (provided by applicant): We propose to establish a Biomedical Technology Research Center (BTRC) in High Performance Computing for Multiscale Modeling of Biological Systems, as a joint effort between the U of Pittsburgh (Pitt; lead institution), Carnegie Mellon U (CMU), the Pittsburgh Supercomputing Center (PSC) and Salk Institute. The Center will develop technology and tools to facilitate research and training at the interface between computing technology and life sciences, and focus on a deeper understanding ofthe molecular and cellular organization and mechanisms that underlie synaptic signaling and regulation, thus facilitating the discovery of new treatments against nervous system disorders. The goal is to start filling the gap between modeling efforts at disparate scales of structural biology, cellular microphysiology and large scale image analysis. Computational technology research and development (TR&D) studies will be conducted in (i) molecular modeling and simulations, (ii) cell modeling and simulations, and (iii) bioimage processing and analysis. These activities will emphasize developing tools to tackle the spatial and molecular complexity inherent in signal transmission and will be driven by five experimental driving biomedical projects (at Pitt, Caltech, Harvard and UT Southwestern Medical Center) on (i) neurotransmitter transport by excitatory amino acid transporters, (ii) activation of CaMKII in spines, (iii) dopamine transporter trafficking in dopamie neurons, (iv) Itk as a regulator of T cell signaling, and (iv) neuronal circuit reconstruction from serial section transmission electron microscopy images. The Center will carry out a vigorous training and dissemination program in its areas of concentration, it will leverage the capabilities of the PSC which has been home to a BTRC for more than twenty years and, besides its biomedical technology research, has a long track record of service, training and dissemination. It will also take advantage ofthe unique strengths ofthe Computational & Systems Biology Department at Pitt, and the Lane Center for Computational Biology at CMU, building on numerous successful collaborative research and training efforts between the two universities, and cutting-edge research at the Computational Neurobiology Laboratory at the Salk Institute.

描述（由申请人提供）：我们建议建立一个生物系统多尺度建模高性能计算生物医学技术研究中心（BTRC），由匹兹堡大学（匹兹堡大学；牵头机构）、卡内基梅隆大学（CMU）、匹兹堡超级计算中心（PSC）和索尔克研究所共同努力。该中心将开发技术和工具，以促进计算技术和生命科学之间的研究和培训，并专注于更深入地了解突触信号传导和调节背后的分子和细胞组织和机制，从而促进发现针对神经系统疾病的新疗法。目标是开始填补结构生物学、细胞微生理学和大规模图像分析不同尺度的建模工作之间的空白。计算技术研发（TR＆D）研究将在（i）分子建模和模拟，（ii）细胞建模和模拟，以及（iii）生物图像处理和分析方面进行。这些活动将强调开发工具来解决信号传输中固有的空间和分子复杂性，并将由五个实验驱动生物医学项目（皮特、加州理工学院、哈佛大学和德克萨斯大学西南医学中心）推动，这些项目涉及（i）兴奋性氨基酸转运蛋白的神经递质转运，（ii）脊柱中CaMKII的激活，（iii）多巴胺中的多巴胺转运蛋白贩运 神经元，(iv) Itk 作为 T 细胞信号传导的调节剂，以及 (iv) 神经元回路重建 连续切片透射电子显微镜图像。该中心将在其重点领域开展积极的培训和传播计划，充分发挥其能力 PSC 的 BTRC 已有二十多年的历史，除了生物医学技术研究之外，在服务、培训和传播方面也有着悠久的记录。它还将利用皮特大学计算与系统生物学系和卡耐基梅隆大学莱恩计算生物学中心的独特优势，以两所大学之间众多成功的合作研究和培训工作以及索尔克研究所计算神经生物学实验室的前沿研究为基础。