COPASI: Biochemical Network Modeling and Simulation Software

描述(申请人提供)：生化网络的建模和模拟已经成为帮助理解细胞行为和促进现代实验的定量解释的基本活动。人们正在倡导一种结合建模、模拟和定量实验的新方法--“系统生物学”。系统生物学的新奇之处在于，实验、数学建模和计算机模拟都是以合作的方式进行的，其中一个的结果将用于另一个的后续迭代。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将模型与实验联系起来。我们建议通过继续开发我们的软件COPASI来解决这一问题和其他系统生物学需求，COPASI是广泛使用的GEPASI的继任者。该项目还将向充满活力的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：使COPASI具有提供高级模型分析的新功能。这将包括增加用于非线性动力学分析的算法，降低模型复杂性，改进参数估计和实验-模型-实验循环的闭合方法，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遵从性。COPASI将帮助用户根据Miriam标准创建和维护模型，并提供在SBW环境中充当客户和提供者的方法。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；将收集和修复错误报告；将收集用户的改进建议并遵循。目标4.支持建模社区。提供在线支持工具，如用户论坛、常见问题解答和维基。将举办一年一度的COPASI用户研讨会。

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.