COPASI software for modeling and simulation of biochemical networks

用于生化网络建模和仿真的 COPASI 软件

• 批准号: 8237359
• 负责人: Pedro Mendes
• 金额: $ 34.35万
• 依托单位: VIRGINIA POLYTECHNIC INST AND ST UNIV
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-09-01 至 2016-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8237359
• 关键词: Address; Adopted; Advocate; Algorithms; Behavior; Biochemical; Biomedical Research; Charge; Code; Collection; Communities; Complement; Computer Simulation; Computer software; Data; Databases; Development; Disease; Disease model; Drug Design; Education; Educational Curriculum; Educational workshop; Equation; Event; Feedback; Filament; Flavoring; Health; Internet; Knowledge Discovery; Language; Linux; Maintenance; Manuals; Medicine; Membrane; Methods; Modeling; Noise; Process; Property; Reading; Reporting; Research; Research Infrastructure; Research Personnel; Running; Science; Software Engineering; Suggestion; System; Systems Biology; Testing; Time; Training; Universities; Visual; Writing; chemical kinetics; commercial application; complex biological systems; computerized tools; data modeling; experience; human disease; improved; interoperability; microbial alkaline proteinase inhibitor; model design; models and simulation; multi-scale modeling; novel strategies; open source; operation; outreach; outreach program; programs; repository; research study; simulation; symposium; two-dimensional; usability; user-friendly; web site

DESCRIPTION (provided by applicant): Modeling and simulation of biochemical networks has become an essential activity to aid in the understanding of cellular behavior and to facilitate quantitative interpretation of modern experiments. A new approach, "systems biology", is being advocated which combines modeling, simulation and quantitative experiments. Biomedical research is becoming increasingly dependent on construction and simulation of computational models. Arguably this will be even more the case with the development of personalized medicine. However, the technical aspects of modeling and simulation are overwhelming to a large number of biomedical researchers, and what is needed is a software application that is capable of providing the appropriate numerical algorithms shielded by a user interface that aides the biomedical researcher to conduct the required simulations. We propose to address this need with continuing development of our software COPASI, which is already widely used in the research community. This project will also provide support to the vibrant community of COPASI users/biomedical researchers. We will address this with the following Specific Aims: Aim 1: Enable COPASI with new functionality to provide advanced model capabilities by adding support for models containing noise and explicit time delays. Support for 1 and 2 dimensional compartments (filaments and membranes) will be implementes as well as support for discrete events in stochastic and delay differential simulation algorithms. Aim 2. Improve and extend interoperability and standards compliance. COPASI will be equipped to facilitate users to create and read simulation information in SED-ML format, it will be enabled to save and read simulation and experimental result in the SBRML format, and it will support the proposed SBML Level 3. Aim 3. Software maintenance. An existing testing plan will be continued and expanded, including appropriate collection models designed to test the various functions of the software; bug reports will be collected and fixed; suggestions for improvement will be collected from users and followed through. Aim 4. Support the modeling community. Online support will be developed and maintained, such as video tutorials, user forum, user manual, and frequently asked questions. A COPASI User's Workshop will be held annually. PUBLIC HEALTH RELEVANCE: This research will focus on developing and maintaining a computational tool, COPASI, for studying complex biological systems, including human disease models. This software application will facilitate knowledge discovery using computer simulations that are important in health and disease, including drug design. Use of this software will be available to all biomedical researchers and will contribute to understanding how diseases develop and how they can be cured.

描述（由申请人提供）：生化网络的建模和模拟已成为帮助理解细胞行为和促进现代实验的定量解释的重要活动。人们正在提倡一种新的方法，即“系统生物学”，它结合了建模、模拟和定量实验。生物医学研究越来越依赖于计算模型的构建和模拟。可以说，随着个性化医疗的发展，情况更是如此。然而，建模和模拟的技术方面对大量生物医学研究人员来说是难以承受的，他们需要的是一种软件应用程序，能够提供适当的数值算法，并由用户界面屏蔽，帮助生物医学研究人员进行所需的模拟。我们建议通过持续开发我们的软件 COPASI 来满足这一需求，该软件已经在研究界广泛使用。该项目还将为充满活力的 COPASI 用户/生物医学研究人员社区提供支持。我们将通过以下具体目标来解决这个问题： 目标 1：通过添加对包含噪声和显式时间延迟的模型的支持，使 COPASI 具有新功能，以提供高级模型功能。将实现对一维和二维隔室（丝和膜）的支持，以及对随机和延迟微分模拟算法中的离散事件的支持。目标 2. 改进和扩展互操作性和标准合规性。 COPASI 将方便用户创建和读取 SED-ML 格式的仿真信息，能够以 SBRML 格式保存和读取仿真和实验结果，并将支持拟议的 SBML Level 3。 目标 3. 软件维护。将继续并扩展现有的测试计划，包括旨在测试软件各种功能的适当收集模型；将收集并修复错误报告；将收集用户的改进建议并予以落实。目标 4. 支持建模社区。将开发和维护在线支持，例如视频教程、用户论坛、用户手册和常见问题。 COPASI 用户研讨会将每年举行一次。 公共健康相关性：这项研究将重点开发和维护计算工具 COPASI，用于研究复杂的生物系统，包括人类疾病模型。该软件应用程序将利用计算机模拟促进知识发现，这对健康和疾病（包括药物设计）很重要。所有生物医学研究人员都可以使用该软件，并将有助于了解疾病如何发展以及如何治愈它们。