Cytoscape 自动化：赋能基于工作流的网络分析。

Department of Medicine, University of California, La Jolla, San Diego, CA, 92093, USA.

University of California, San Francisco, San Francisco, CA, 94143, USA.

Genome Biol. 2019 Sep 2;20(1):185. doi: 10.1186/s13059-019-1758-4.

Cytoscape is one of the most successful network biology analysis and visualization tools, but because of its interactive nature, its role in creating reproducible, scalable, and novel workflows has been limited. We describe Cytoscape Automation (CA), which marries Cytoscape to highly productive workflow systems, for example, Python/R in Jupyter/RStudio. We expose over 270 Cytoscape core functions and 34 Cytoscape apps as REST-callable functions with standardized JSON interfaces backed by Swagger documentation. Independent projects to create and publish Python/R native CA interface libraries have reached an advanced stage, and a number of automation workflows are already published.

Cytoscape 是最成功的网络生物学分析和可视化工具之一，但由于其交互性质，其在创建可重复、可扩展和新颖工作流程方面的作用受到限制。我们描述了 Cytoscape Automation (CA)，它将 Cytoscape 与高效的工作流程系统（例如 Jupyter/RStudio 中的 Python/R）结合在一起。我们将超过 270 个 Cytoscape 核心功能和 34 个 Cytoscape 应用程序作为可通过 REST 调用的函数公开，这些函数具有标准化的 JSON 接口，并由 Swagger 文档提供支持。创建和发布 Python/R 本机 CA 接口库的独立项目已经进入高级阶段，并且已经发布了许多自动化工作流程。