GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research.
GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research.
复制标题
DOI：
10.1371/journal.pone.0152686
复制
发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Yeung KY
中科院分区：
文献类型：
--
作者：
Hung LH;Kristiyanto D;Lee SB;Yeung KY
可重复性在科学中至关重要。对于复杂的计算方法，通常不仅需要重新创建代码，还需要软件和硬件环境来重新生成结果。无论底层硬件和操作系统如何，虚拟机和容器软件(如Docker)都可以重现准确的环境。然而，使用图形用户界面(GUI)的工作流仍然难以在不同的主机系统上复制，因为没有对所有平台通用的高级图形软件层。GUIdock允许轻松地分发系统生物学应用程序及其图形环境。基于图形的复杂工作流在系统生物学中无处不在，现在可以很容易地在许多不同的平台上导出和复制。GUIdock使用Docker，这是一个开源项目，它提供了一个仅具有绝对必要的软件依赖项的容器，并在Linux、Macintosh和Windows平台上配置了一个通用的X Windows(X11)图形界面。作为概念的证明，我们提供了一个Docker包，其中包含一个用R和C++编写的名为networkBMA的BioConductor应用程序，用于基因网络推理。我们的产品包还包括Cytosscape，这是一个基于Java的平台，具有用于可视化和分析基因网络的图形用户界面，以及CyNetworkBMA应用程序，它是一款Cytosscape应用程序，允许通过用户友好的Cytoscape界面使用networkBMA。
Reproducibility is vital in science. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results. Virtual machines, and container software such as Docker, make it possible to reproduce the exact environment regardless of the underlying hardware and operating system. However, workflows that use Graphical User Interfaces (GUIs) remain difficult to replicate on different host systems as there is no high level graphical software layer common to all platforms. GUIdock allows for the facile distribution of a systems biology application along with its graphics environment. Complex graphics based workflows, ubiquitous in systems biology, can now be easily exported and reproduced on many different platforms. GUIdock uses Docker, an open source project that provides a container with only the absolutely necessary software dependencies and configures a common X Windows (X11) graphic interface on Linux, Macintosh and Windows platforms. As proof of concept, we present a Docker package that contains a Bioconductor application written in R and C++ called networkBMA for gene network inference. Our package also includes Cytoscape, a java-based platform with a graphical user interface for visualizing and analyzing gene networks, and the CyNetworkBMA app, a Cytoscape app that allows the use of networkBMA via the user-friendly Cytoscape interface.