Software Integration between JSim and Systems Biology Workbench

JSim 和 Systems Biology Workbench 之间的软件集成

• 批准号: 8088092
• 负责人: JAMES B BASSINGTHWAIGHTE
• 金额: $ 32.37万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-06-01 至 2013-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8088092
• 关键词: Algorithms; Archives; Basic Science; Behavior; Behavioral; Biochemical; Biochemical Reaction; Biological; Biological Models; Biology; Cell physiology; Code; Communities; Complex; Computer software; Confidence Intervals; Data; Data Analyses; Data Files; Databases; Dependency; Elements; Environment; Enzymes; Equation; Equilibrium; Event; Fostering; Generations; Genetic; Genomics; Health; Health Benefit; Imagery; Individual; Java; Kinetics; Language; Libraries; Link; Linux; Liquid substance; Maps; Mechanics; Metabolism; Methodology; Methods; Modeling; Molecular Biology; Monte Carlo Method; Noise; Ontology; Organ; Output; Pharmacology; Phosphorylation; Physiological; Physiology; Protons; Public Health; Reaction; Regulation; Research; Research Personnel; Running; Solid; Solutions; Source Code; Specific qualifier value; Structure; System; Systems Biology; Techniques; Temperature; Thermodynamics; Time; Training; Translations; Universities; Update; Variant; Washington; Wisconsin; base; biological systems; clinical application; clinical practice; complex biological systems; design; experience; file format; improved; interoperability; medical schools; microbial alkaline proteinase inhibitor; multi-scale modeling; open source; parallel computing; programs; reaction rate; research study; simulation; software development; therapy outcome; tool

DESCRIPTION (provided by applicant): This software development project combines the perspectives and software from three experienced groups to create and maintain what will be the most advanced and complete software package available for systems biology and the analysis of physiological data for research and clinical practice. The project brings together: (1) The JSim system for model based analysis using single or multi-scale models using ordinary and 1- dimensional partial differential equations for transport and metabolism (Butterworth and Bassingthwaighte, University of Washington), (2) the System Biology Workbench and related software coding packages invented by Herbert Sauro (Unversity of Washington), and (3) thermodynamically constrained and detailed equations for biochemical reactions created automatically from databases on reactions equilibria and kinetics (Daniel Beard, Medical College Wisconsin). The coalescence of these three powerful techniques, all of which utilize archival database markup languages like SBML and CellML, will foster model construction using JSim's inbuilt error identification and correction mechanisms. The toolkits and models will be disseminated worldwide in easily understood code, and will provide exactly and directly reproducible solutions on a wide range of computational platforms including Windows, Macintosh, and Linux. The models will be designed for experiment design and analysis, and the open source code for models and the analysis packages will be freely available to investigators everywhere. This powerful combination is relevant to the betterment of health as it provides investigators in genomics, molecular biology, physiology, and pharmacology with practical mechanisms for predicting and understanding integrated cellular organ and body function. Many of the current generation of biologists are not deeply trained in quantitative analysis of complex systems, so the availability of these tools will greatly facilitate their understanding of the biology and their ability to design more precisely targeted experimentation, more efficient data analysis, and improved therapies. PUBLIC HEALTH RELEVANCE: This research will expedite the translation from basic research in genomics, genetic network regulation, biochemical network behavior, and cell function to clinical applications that provide long range public health benefits. It will occur via better directed experimentation through modeling, and through improved prediction of therapy outcomes.

描述（由申请人提供）：该软件开发项目结合了三个经验丰富的团队的观点和软件，以创建和维护最先进、最完整的软件包，可用于系统生物学以及研究和临床实践的生理数据分析。该项目汇集了：(1) JSim 系统，用于使用单尺度或多尺度模型进行基于模型的分析，使用普通和一维偏微分方程进行运输和新陈代谢（Butterworth 和 Bassingthwaighte，华盛顿大学），(2) 该系统Herbert Sauro（华盛顿大学）发明的 Biology Workbench 和相关软件编码包，以及 (3) 从反应平衡和动力学数据库自动创建的生化反应的热力学约束和详细方程（丹尼尔·比尔德，威斯康星医学院）。这三种强大技术的结合，所有这些技术都利用档案数据库标记语言，如 SBML 和 CellML，将促进使用 JSim 内置错误识别和纠正机制的模型构建。这些工具包和模型将以易于理解的代码在全球范围内传播，并将在包括 Windows、Macintosh 和 Linux 在内的各种计算平台上提供准确且直接可重现的解决方案。这些模型将用于实验设计和分析，模型和分析包的开源代码将免费提供给世界各地的研究人员。这种强大的组合与改善健康相关，因为它为基因组学、分子生物学、生理学和药理学的研究人员提供了预测和理解综合细胞器官和身体功能的实用机制。当代许多生物学家没有接受过复杂系统定量分析方面的深入培训，因此这些工具的可用性将极大地促进他们对生物学的理解以及设计更精确的针对性实验、更有效的数据分析和改进疗法的能力。公共健康相关性：这项研究将加快基因组学、遗传网络调控、生化网络行为和细胞功能等基础研究向临床应用的转化，从而提供长期的公共健康益处。它将通过通过建模进行更好的定向实验以及通过改进治疗结果的预测来实现。