COPASI - Open source software for advanced biochemical network modelling

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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.