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Abstract：
Interactive Jupyter Notebooks in combination with Conda environments can be used to generate FAIR (Findable, Accessible, Interoperable and Reusable/Reproducible) biomolecular simulation workflows. The interactive programming code accompanied by documentation and the possibility to inspect intermediate results with versatile graphical charts and data visualization is very helpful, especially in iterative processes, where parameters might be adjusted to a particular system of interest. This work presents a collection of FAIR notebooks covering various areas of the biomolecular simulation field, such as molecular dynamics (MD), protein-ligand docking, molecular checking/modeling, molecular interactions, and free energy perturbations. Workflows can be launched with myBinder or easily installed in a local system. The collection of notebooks aims to provide a compilation of demonstration workflows, and it is continuously updated and expanded with examples using new methodologies and tools.
摘要：
交互式JupyterNotebooks结合Conda环境可用于生成FAIR(Findable,可访问,可互操作和可重用/可复制)生物分子模拟工作流程。带有文档的交互式编程代码以及使用通用图形图表和数据可视化检查中间结果的可能性非常有用，尤其是在迭代过程中，其中参数可能会根据感兴趣的特定系统进行调整。这项工作提供了涵盖生物分子模拟领域各个领域的FAIR笔记本集合，如分子动力学(MD)，蛋白质-配体对接，分子检查/建模，分子相互作用，和自由能扰动。工作流可以使用myBinder启动，也可以轻松安装在本地系统中。本集旨在提供示范工作流程的汇编,并使用新的方法和工具不断更新和扩展示例。
