Software Integration between JSim and Systems Biology Workbench

JSim 和 Systems Biology Workbench 之间的软件集成

• 批准号: 8274847
• 负责人: JAMES B BASSINGTHWAIGHTE
• 金额: $ 32.5万
• 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/8274847
• 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

Project Summary 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.

项目概要 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 创建和维护可用于系统的最先进、最完整的软件包 用于研究和临床实践的生物学和生理数据分析。该项目汇集了：（1） JSim 系统使用普通模型和 1-模型进行基于模型的分析，使用单尺度或多尺度模型 运输和新陈代谢的多维偏微分方程（Butterworth 和 Bassingthwaighte， 华盛顿大学），（2）发明了系统生物学工作台和相关软件编码包 作者：Herbert Sauro（华盛顿大学），以及 (3) 热力学约束和详细方程 根据反应平衡和动力学数据库自动创建生化反应（Daniel Beard， 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 SBML 和 CellML 等数据库标记语言将使用 JSim 的内置错误促进模型构建 识别和纠正机制。这些工具包和模型将在全球范围内轻松传播 理解的代码，并将在广泛的计算上提供准确且直接可重现的解决方案 平台包括 Windows、Macintosh 和 Linux。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 到处都有调查员。这种强大的组合与改善健康相关，因为它提供了 基因组学、分子生物学、生理学和药理学的研究人员，具有实用的机制 预测和理解综合细胞器官和身体功能。当前这一代人中的许多人 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他们设计更精确目标的能力 实验、更有效的数据分析和改进的疗法。