COPASI - Open source software for advanced biochemical network modelling

生物化学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定量解释的重要活动。一种新的生物科学方法，“系统生物学”正在被提倡，它结合了建模，模拟和定量实验。生物科学研究越来越依赖于计算模型的构建和模拟。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，帮助研究人员进行所需的模拟。我们通过不断开发我们的软件COPASI来满足这一需求，该软件已在研究界得到广泛应用。该项目还将为英国生物科学研究界充满活力的COPASI用户社区提供支持。在这个项目中，我们将扩展COPASI的功能：我们将添加方法来模拟具有显式时间延迟的模型;提供一种简单计算整个模拟和模拟组摘要的机制;整合了一个新功能，使研究人员首次能够浏览模型的整个历史，从而正式确定发生变化的原因，该项目还将改进和扩展软件的互操作性和标准遵从性。这对于生物科学研究人员自由交换数据和模型至关重要。COPASI将配备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，并支持拟议的SBML Level 3（表示生物模型的格式）。我们将继续使用正式的软件开发方法来开发COPASI，以提高质量。现有的测试计划将继续和扩大，包括适当收集模型，旨在测试软件的各种功能;将收集和修复错误报告;将收集用户的改进建议，并贯彻到底。最后，我们的目标是支持生物科学界使用COPASI和建模和模拟一般。将开发和维护在线支持，如视频教程、网络支持论坛和用户手册。我们将每年举办两次COPASI用户研讨会，生物科学研究人员在此学习使用软件的新功能，在开发团队的帮助下将其应用于他们的问题，并提出改进建议。我们还将在流行的系统生物学会议上提供教程。

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 to biological sciences, "systems biology", is being advocated which combines modeling, simulation and quantitative experiments. Bioscience research is becoming increasingly dependent on construction and simulation of computational models. 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 researcher to conduct the required simulations. We address this need here 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 in the UK bioscience research community. In this project we will extend the capabilities of COPASI: we will add means to simulate models with explicit time delays; provide a mechanism for easy calculation of summaries of entire simulations and groups of simulations; incorporate a new feature that will allow researchers, for the first time, to be able to navigate the entire history of a model, such that the reasons for changes that took place are formally identified, as well as decisions on the model structure.The project will also improve and extend the software's interoperability and standards compliance. This is extremely important in order to allow bioscience researchers to freely exchange data and models. 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 (a format to represent biological models).We will keep developing COPASI using formal software development methodologies that promote quality. An existing testing plan will be continued and expanded, including appropriate collection of 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.Finally we aim to support the bioscience community in their use of COPASI and modelling and simulation in general. Online support will be developed and maintained, such as video tutorials, a web support forum, and a user manual. We will hold COPASI User Workshops twice yearly, where bioscience researchers learn to use new features of the software, apply it to their problems with help from the development team, and present their suggestions for improvement. We will also provide tutorials at popular systems biology conferences.