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: 9118310
• 负责人: Ivet Bahar
• 金额: $ 155.73万
• 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/9118310
• 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 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; microscopic imaging; models and simulation; molecular modeling; multi-scale modeling; nervous system disorder; neuronal circuitry; neurotransmitter transport; program dissemination; 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）：我们建议在高性能计算中建立生物医学技术研究中心（BTRC），以用于生物系统的多尺度建模，作为匹兹堡U（Pitt; Pitt; Lead Institation），Carnegie Mellon U（CMU）的联合努力，匹兹堡Mellon U（CMU），匹兹堡超级计算中心（PSC）和Salk Instutt和Salk Instutt和Salk Instutt。该中心将开发技术和工具，以促进计算技术与生命科学之间的界面上的研究和培训，并着重于对分子和细胞组织的更深入理解，以及基于突触信号传导和调节的机制，从而促进发现新治疗对针对神经系统疾病的发现。目的是开始填补结构生物学，细胞微生物生理学和大规模图像分析的不同尺度的建模工作之间的差距。计算技术研发（TR＆D）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中进行研究。这些活动将强调开发信号传输中固有的空间和分子复杂性的工具，并将受到五个实验性驾驶生物医学项目（在Pitt，Pitt，Caltech，Harvard和UT Southertern Medical Center）对（I）神经递质通过兴奋性氨基酸转运蛋白（（II）Camkii Inii Inii inii inii inii in（II III）的神经递质运输（III）（III）（II III II III），（II III）（II III II II II）。神经元，（iv）ITK作为T细胞信号的调节剂，（iv）神经元电路重建 串行部分传输电子显微镜图像。该中心将在其集中度领域进行大力培训和传播计划，它将利用能力 在BTRC的PSC中，已有二十多年了，除了其生物医学技术研究外，还具有长期的服务，培训和传播记录。它还将利用Pitt的计算与系统生物学系的独特优势，以及CMU的巷计算生物学中心，建立了两所大学之间的许多成功的合作研究和培训工作，以及Salk Institute的计算神经生物学实验室的尖端研究。