COPASI: Biochemical Network Modeling and Simulation Software

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。系统生物学的新奇之处在于，实验、数学建模和计算机模拟是以一种合作的方式进行的，其中一种方法的结果被用于其他方法的后续迭代。可以说，为了实现系统生物学的承诺，需要软件工具能够适当地连接模型和实验。我们建议解决这一问题，以及其他系统生物学的需求，继续开发我们的软件COPASI，这是广泛使用的Gepasi的继任者。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：使COPASI具有新的功能，以提供高级模型分析。这将包括增加非线性动力学分析算法、降低模型复杂性、改进参数估计和闭合实验-模型-实验循环的方法，以及某些算法的并行化。目标2.改进和扩展互操作性和标准合规性。COPASI将配备，以方便用户创建和维护模型根据MIRIAM标准，并与方法，作为一个客户端和提供商在SBW环境。SBML支持将继续并得到加强。目标3。软件维护。将制定测试计划，包括适当的测试套件和程序;将收集并修复错误报告;将从用户那里收集并遵循改进建议。目标4。支持建模社区。提供在线支持工具，如用户论坛、FAQ和Wiki。将举办COPASI用户年度讲习班。

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. The novelty of systems biology is that experiments, mathematical modeling, and computer simulation are practiced in a cooperative way, the results of one being used for subsequent iterations of the others. Arguably, to fulfill the promise of systems biology there is a need for software tools to be able to appropriately connect models to experiments. We propose to address this, and other systems biology needs, with continuing development of our software COPASI, which is the successor of the widely used Gepasi. 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 analyses. This will include adding algorithms for nonlinear dynamical analysis, model complexity reduction, improved parameter estimation and methods for closing the loop of experiment-model-experiment, and parallelization of certain algorithms. Aim 2. Improve and extend interoperability and standards compliance. COPASI will be equipped to facilitate users to create and maintain models according to the MIRIAM standard, and with methods to act as a client and provider in the SBW environment. SBML support will continue and be enhanced. Aim 3. Software maintenance. A testing plan will be established, including appropriate testing suites and procedures; bug reports will be collected and fixed; suggestions for improvement will be collected from users and followed. Aim 4. Support the modeling community. Providing online support tools, such as a user forum, FAQ and Wiki. An Annual COPASI User's Workshop will be held.