Building applications for interactive data exploration in systems biology
Building applications for interactive data exploration in systems biology
复制标题
构建系统生物学中交互式数据探索的应用程序
DOI：
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发表时间：
2017
期刊：
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通讯作者：
L. A. Bongo
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作者：
Bjørn Fjukstad;V. Dumeaux;K. Olsen;Michael Hallet;E. Lund;L. A. Bongo
随着系统生物界以前所未有的速度生成和收集数据，人们越来越需要交互式数据探索工具来探索数据集。这些工具需要结合先进的统计分析、来自生物数据库的相关知识，以及具有清晰用户界面的应用程序中的交互式可视化。要回答特定的研究问题，工具必须提供专门的用户界面和可视化。虽然这些组件是特定于应用程序的，但数据分析工具的底层组件可以在以后共享和重用。因此，应用程序开发人员可以组合可重用服务的应用程序，而不是从头开始为每个项目实现单一的整体应用程序。我们在系统生物学中开发数据探索应用程序的方法建立在微服务体系结构上。微服务体系结构将应用程序分成较小的组件，这些组件使用与语言无关的协议进行通信。我们表明，这种设计适合于生物信息学应用程序，其中应用程序经常使用不同的工具，由不同的研究小组用不同的语言编写。将每个服务打包到软件容器中，可以在应用程序之间重用和共享关键组件，从而减少开发、部署和维护时间。我们通过一个名为Mixt血液-肿瘤的网络应用程序展示了我们方法的可行性，该应用程序用于探索和比较乳腺癌患者血液和肿瘤样本的转录图谱。该应用程序集成了先进的统计软件、生物数据库的最新信息和现代数据可视化库。用于研究转录特征的网络应用程序Mixt在线地址为Mixt-hemal-tomor.bci.mcgill.ca，开源地址为gihub.com/fjukstad/Mixt。构建支持微服务的包是作为Kvik的一部分开源的，请访问githorb.com/fjukstad/kvik。
As the systems biology community generates and collects data at an unprecedented rate, there is a growing need for interactive data exploration tools to explore the datasets. These tools need to combine advanced statistical analyses, relevant knowledge from biological databases, and interactive visualizations in an application with clear user interfaces. To answer specific research questions tools must provide specialized user interfaces and visualizations. While these are application-specific, the underlying components of a data analysis tool can be shared and reused later. Application developers can therefore compose applications of reusable services rather than implementing a single monolithic application from the ground up for each project. Our approach for developing data exploration applications in systems biology builds on the microservice architecture. Microservice architectures separates an application into smaller components that communicate using language-agnostic protocols. We show that this design is suitable in bioinformatics applications where applications often use different tools, written in different languages, by different research groups. Packaging each service in a software container enables re-use and sharing of key components between applications, reducing development, deployment, and maintenance time. We demonstrate the viability of our approach through a web application, MIxT blood-tumor, for exploring and comparing transcriptional profiles from blood and tumor samples in breast cancer patients. The application integrates advanced statistical software, up-to-date information from biological databases, and modern data visualization libraries. The web application for exploring transcriptional profiles, MIxT, is online at mixt-blood-tumor.bci.mcgill.ca and open-sourced at github.com/fjukstad/mixt. Packages to build the supporting microservices are open-sourced as a part of Kvik at github.com/fjukstad/kvik.