COPASI - Open source software for advanced biochemical network modelling

COPASI - 用于高级生化网络建模的开源软件

• 批准号: BB/J019259/1
• 负责人: Pedro Mendes
• 金额: $ 80.06万
• 依托单位: University of Manchester
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2012
• 资助国家: 英国
• 起止时间: 2012 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FJ019259%2F1
• 关键词: COPASI; Open; source; software; advanced

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.

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对现代实验的定量解释的一项基本活动。人们正在倡导一种新的生物科学方法--“系统生物学”，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，建模和模拟的技术方面对大量生物医学研究人员来说是压倒一切的，所需要的是一种软件应用程序，该软件应用程序能够提供由用户界面屏蔽的适当的数值算法，该用户界面帮助研究人员进行所需的模拟。我们在这里通过不断开发我们的软件COPASI来满足这一需求，该软件已经在研究界广泛使用。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：我们将增加模拟具有显式时间延迟的模型的方法；提供一种机制来方便地计算整个模拟和模拟组的汇总；加入一个新功能，使研究人员第一次能够导航模型的整个历史，以便正式确定发生变化的原因，以及关于模型结构的决策。该项目还将改进和扩展软件的互操作性和标准遵从性。为了让生物科学研究人员自由交换数据和模型，这是极其重要的。COPASI将便于用户创建和读取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 Level 3(一种表示生物模型的格式)。我们将继续使用提高质量的正式软件开发方法来开发COPASI。将继续并扩大现有的测试计划，包括收集适当的模型以测试软件的各种功能；将收集和修复错误报告；收集用户的改进建议并进行跟踪。最后，我们的目标是支持生物科学界使用COPASI以及一般的建模和模拟。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，在那里生物科学研究人员学习使用该软件的新功能，在开发团队的帮助下将其应用于他们的问题，并提出他们的改进建议。我们还将在流行的系统生物学会议上提供教程。

项目成果

What can we learn from global sensitivity analysis of biochemical systems?

• DOI: 10.1371/journal.pone.0079244
• 发表时间: 2013
• 期刊: PloS one
• 影响因子: 3.7
• 作者: Kent E;Neumann S;Kummer U;Mendes P
• 通讯作者: Mendes P

Fitting Transporter Activities to Cellular Drug Concentrations and Fluxes: Why the Bumblebee Can Fly.

• DOI: 10.1016/j.tips.2015.07.006
• 发表时间: 2015-11
• 期刊: Trends in pharmacological sciences
• 影响因子: 13.8
• 作者: Mendes P;Oliver SG;Kell DB
• 通讯作者: Kell DB

Path2Models: large-scale generation of computational models from biochemical pathway maps.

• DOI: 10.1186/1752-0509-7-116
• 发表时间: 2013-11-01
• 期刊: BMC systems biology
• 作者: Büchel F;Rodriguez N;Swainston N;Wrzodek C;Czauderna T;Keller R;Mittag F;Schubert M;Glont M;Golebiewski M;van Iersel M;Keating S;Rall M;Wybrow M;Hermjakob H;Hucka M;Kell DB;Müller W;Mendes P;Zell A;Chaouiya C;Saez-Rodriguez J;Schreiber F;Laibe C;Dräger A;Le Novère N
• 通讯作者: Le Novère N

COPASI and its applications in biotechnology.

• DOI: 10.1016/j.jbiotec.2017.06.1200
• 发表时间: 2017-11-10
• 期刊: Journal of biotechnology
• 影响因子: 4.1
• 作者: Bergmann FT;Hoops S;Klahn B;Kummer U;Mendes P;Pahle J;Sahle S
• 通讯作者: Sahle S

A computational model of liver iron metabolism.

• DOI: 10.1371/journal.pcbi.1003299
• 发表时间: 2013
• 期刊: PLoS computational biology
• 影响因子: 4.3
• 作者: Mitchell S;Mendes P
• 通讯作者: Mendes P