Software Integration between JSim and Systems Biology Workbench

JSim 和 Systems Biology Workbench 之间的软件集成

• 批准号: 7844809
• 负责人: JAMES B BASSINGTHWAIGHTE
• 金额: $ 33.44万
• 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/7844809
• 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; public health relevance; 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小组的观点和软件，以创建和维护最先进和完整的软件包，可用于系统生物学以及用于研究和临床实践的生理数据分析。该项目汇集了：（1）使用单一或多尺度模型的JSIM系统，使用普通和1维偏微分方程进行运输和代谢（Butterworth and Bassingthwaighte，华盛顿大学），（2）System Bibench and System Bibench and System Biberology Working for Herbert Sauro（Herbert Sauro（Herbert Sauro）（3），以及详细信息（Uneveral）（3）生化反应自动从有关反应平衡和动力学的数据库（威斯康星州医学院）自动产生。这三种功能强大的技术的合并，所有这些技术都利用了档案数据库标记语言，例如SBML和CellML，将使用JSIM的内置错误识别和校正机制来促进模型构建。工具包和模型将在易于理解的代码中在全球范围内传播，并将在包括Windows，Macintosh和Linux在内的广泛计算平台上提供准确，直接可重现的解决方案。这些模型将用于实验设计和分析，并且模型的开源代码和分析软件包将免费提供给各地的调查人员。这种强大的组合与健康的改善有关，因为它为研究人员提供了基因组学，分子生物学，生理学和药理学的研究，并具有预测和理解综合细胞器官和人体功能的实用机制。许多当前一代的生物学家没有对复杂系统的定量分析进行深入培训，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及其设计更精确的靶向实验，更有效的数据分析和改进的治疗能力。公共卫生相关性：这项研究将加快从基因组学基础研究，遗传网络调节，生化网络行为和细胞功能到提供长期公共健康益处的临床应用的转化。它将通过建模和改进治疗结果预测通过更好的定向实验。