Biological Information Processing Group, BioQuant, Heidelberg University; BQ47, INF267, 69120 Heidelberg, Germany.
Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ); INF280, 69120 Heidelberg, Germany; Molecular Vaccine Design, German Center for Infection Research (DZIF), partner site Heidelberg, Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.
Math Biosci. 2022 Jun;348:108822. doi: 10.1016/j.mbs.2022.108822. Epub 2022 Apr 20.
In this article we show how dynamic publication media and the COPASI R Connector (CoRC) can be combined in a natural and synergistic way to communicate (biochemical) models. Dynamic publication media are becoming a popular tool for authors to effectively compose and publish their work. They are built from templates and the final documents are created dynamically. In addition, they can also be interactive. Working with dynamic publication media is made easy with the programming environment R via its integration with tools such as R Markdown, Jupyter and Shiny. Additionally, the COmplex PAthway SImulator COPASI (http://www.copasi.org), a widely used biochemical modelling toolkit, is available in R through the use of the COPASI R Connector (CoRC, https://jpahle.github.io/CoRC). Models are a common tool in the mathematical biosciences, in particular kinetic models of biochemical networks in (computational) systems biology. We focus on three application areas of dynamic publication media and CoRC: Documentation (reproducible workflows), Teaching (creating self-paced lessons) and Science Communication (immersive and engaging presentation). To illustrate these, we created six dynamic document examples in the form of R Markdown and Jupyter notebooks, hosted on the platforms GitHub, shinyapps.io, Google Colaboratory. Having code and output in one place, creating documents in template-form and the option of interactivity make the combination of dynamic documents and CoRC a versatile tool. All our example documents are freely available at https://jpahle.github.io/DynamiCoRC under the Creative Commons BY 4.0 licence.
在本文中，我们展示了如何将动态出版媒体和 COPASI R 连接器（CoRC）以自然和协同的方式结合起来，以交流（生化）模型。动态出版媒体正在成为作者有效组合和发布作品的流行工具。它们是由模板构建的，最终文档是动态创建的。此外，它们还可以具有交互性。通过将编程环境 R 与其集成的工具（如 R Markdown、Jupyter 和 Shiny）一起使用，使用动态出版媒体变得很容易。此外，广泛用于生化建模工具包的 COmplex PAthway SImulator COPASI（http://www.copasi.org）可通过使用 COPASI R 连接器（CoRC，https://jpahle.github.io/CoRC）在 R 中使用。模型是数学生物科学中的常用工具，特别是生化网络的动力学模型在（计算）系统生物学中。我们专注于动态出版媒体和 CoRC 的三个应用领域：文档（可重现的工作流程）、教学（创建自我导向的课程）和科学传播（沉浸式和引人入胜的演示）。为了说明这些，我们以 R Markdown 和 Jupyter 笔记本的形式创建了六个动态文档示例，托管在 GitHub、shinyapps.io 和 Google Colaboratory 平台上。将代码和输出放在一个地方，以模板形式创建文档以及交互选项，使动态文档和 CoRC 的组合成为一种多功能工具。我们的所有示例文档都可以在 https://jpahle.github.io/DynamiCoRC 上免费获得，根据知识共享署名 4.0 许可。
