High Performance Simulation Libraries for Systems Biology

系统生物学的高性能仿真库

• 批准号: 10020192
• 负责人: HERBERT M. SAURO
• 金额: $ 43.34万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-15 至 2023-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10020192
• 关键词: Area; Biochemical; Biochemical Reaction; Biomedical Research; Cell physiology; Cells; Code; Collaborations; Communities; Computer Models; Computer software; Computers; Conscious; Data; Development; Discipline; Disease; Documentation; Education and Outreach; Educational workshop; Generations; Hybrids; Individual; Infrastructure; Kinetics; Letters; Libraries; Maintenance; Maps; Metabolic; Modeling; Organ; Organ Model; Performance; Pharmacologic Substance; Pythons; Reaction; Research Personnel; Running; Scheme; Silicon; Speed; Structural Models; Structure; Supercomputing; System; Systems Biology; Techniques; Technology; Time; Tissue Model; Tissues; Training; Translating; Update; Variant; Water; Weather; Work; analog; base; cluster computing; computer cluster; cost; cost effective; digital; experimental study; flexibility; hydrology; improved; innovation; interactive computing; interest; multi-scale modeling; new technology; next generation; novel; novel strategies; predictive tools; programs; real time model; research and development; simulation; simulation software; tool

Abstract Quantitative analysis and simulation of cellular processes is becoming an important and indispensible tool for predictive biomedical research. Not only that, but models are becoming larger, more sophisticated and encompassing areas such as multicellular and multiscale modeling of tissues and whole organs. Performance can be improved by using compute clusters or the cloud, however interactive computing is severely restricted using this kind of infrastructure. Moreover supercomputing or cloud access is not available to everyone. In this proposal we wish to focus on developing high performance simulators, notably libRoadRunner and specific hardware based on analog computing. libRoadRunner is unique in that it is the only cellular simulator that compiles standard SBML using LLVM. LLVM is a backend machine code generation technology that is starting to be widely used by performance conscious software developers. Using this technology we have achieved significant, in some cases orders of magnitude speed ups in simulation times compared to existing simulators. Our letters of support highlight some of the major improvements that have been realized by this new technology. We have shown that the performance of libRoadRunner is on par (within 95%) with natively compiled solutions. In other words we have reached the limit to computing on ordinary desktop computers. In this proposal we will continue to improve libRoadRunner and implement a completely novel way to carry out cellular simulations which will lead to additional orders of magnitude improvements in simulation performance. Our proposal is to work with Rahul Sarpeshkar at Dartmouth who has pioneered hardware based simulation technologies called cytomorphic computing. As part of this proposal, the Dartmouth group will develop a new generation of ultra-high-speed hardware-based biochemical simulators. We will develop SBML and MATLAB translators that can translate a model directly into programmable high-performance cytomorphic silicon chips. In addition to this highly innovative approach we will also exploit this hardware to implement novel approaches to interactive real-time modeling of cellular processes that includes the complete control of time and temporal incursion. A small part of the proposed effort will include general maintenance of our existing infrastructure as well as organizing an annual workshop on modeling and training.

抽象的 细胞过程的定量分析和模拟正在成为重要且不可或缺的工具 预测性生物医学研究。不仅如此，模型变得越来越大、越来越复杂、越来越复杂。 涵盖组织和整个器官的多细胞和多尺度建模等领域。表现 可以通过使用计算集群或云来改进，但是交互式计算受到严格限制 使用这种基础设施。此外，并非每个人都可以使用超级计算或云访问。在这个 我们希望专注于开发高性能模拟器，特别​​是 libRoadRunner 和特定的 基于模拟计算的硬件。 libRoadRunner 的独特之处在于它是唯一的蜂窝模拟器 使用 LLVM 编译标准 SBML。 LLVM是一种正在起步的后端机器代码生成技术 被注重性能的软件开发人员广泛使用。利用这项技术我们已经实现了 与现有模拟器相比，在某些情况下，模拟时间显着加快了几个数量级。 我们的支持信强调了这一新产品所实现的一些重大改进 技术。我们已经证明 libRoadRunner 的性能与原生的性能相当（95% 以内） 编译的解决方案。换句话说，我们已经达到了普通台式电脑的计算极限。 在这个提案中，我们将继续改进 libRoadRunner 并实现一种全新的方式来执行 细胞模拟，这将导致模拟性能额外数量级的提高。 我们的建议是与达特茅斯学院的 Rahul Sarpeshkar 合作，他是基于硬件的模拟的先驱 称为细胞形态计算的技术。作为该提案的一部分，达特茅斯小组将开发一种新的 新一代基于硬件的超高速生化模拟器。我们将开发SBML和MATLAB 转换器可以将模型直接转换为可编程高性能细胞形态硅芯片。 除了这种高度创新的方法之外，我们还将利用该硬件来实施新颖的方法 细胞过程的交互式实时建模，包括对时间和时间的完全控制 侵入。拟议工作的一小部分将包括对我们现有基础设施的一般维护 并组织年度建模和培训研讨会。