COPASI software for modeling and simulation of biochemical networks

描述（由申请人提供）：生物化学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定量解释的重要活动。一种新的方法，“系统生物学”正在提倡，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，情况将更加如此。然而，建模和仿真的技术方面是压倒了大量的生物医学研究人员，什么是需要的是一个软件应用程序，能够提供适当的数值算法屏蔽的用户界面，帮助生物医学研究人员进行所需的模拟。我们建议继续开发我们的软件COPASI，这已经在研究界广泛使用，以满足这一需求。该项目还将向COPASI用户/生物医学研究人员的活跃社区提供支持。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具有新的功能，以提供高级模型功能。支持1和2维隔间（丝和膜）将implementes以及支持离散事件的随机和延迟差分模拟算法。目标2.改进和扩展互操作性和标准合规性。COPASI将配备以方便用户创建和读取SED-ML格式的模拟信息，它将能够以SBRML格式保存和读取模拟和实验结果，并将支持拟议的SBML 3级。目标3.软件维护。将继续执行并扩大现有的测试计划，包括为测试软件的各种功能而设计的适当收集模式;将收集并修复错误报告;将收集用户提出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，如视频教程、用户论坛、用户手册和常见问题解答。每年将举办COPASI用户讲习班。

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.