At a minimum, Docker for Mac requires macOS Yosemite 10.10.3 or newer, with the caveat that going forward 10.10.x is a use-at-your-own risk proposition. Download google chrome mac version. Starting with Docker for Mac Stable release 1.13, and concurrent Edge releases, we no longer address issues specific to macOS Yosemite 10.10. S1 Video: Demonstration of GUIdock on Linux, Mac OS and Windows. In this video, we ran GUIdock on the same sample dataset across Linux, Mac OS and Windows. We demonstrate that identical gene networks were derived in each operating system. We chose a 9-gene subset of the human cancer RNAseq data from Klijn et al. Among these 9 genes, (CDKN2A, CDKN2B, CCNE1, CCND1) belong to the cell cycle pathway and (ZRSR2, U2AF1, U2AF2, SRSF2, SF3A1) belong to the splicing pathway as indicated in Supplementary Table 12 in Klijn et al. This video is also available on YouTube at. 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. Introduction Reproducibility is a vital feature in science [, ]. Recent articles in the June 26 issue of Science discussed how rarely published results can be reproduced across different disciplines [, ]. Nosek and colleagues proposed guidelines consisting of eight standards and three levels to promote transparency, openness and reproducibility in scientific publications []. These guidelines progress from level 0 to level 3 and become increasingly stringent for each standard (see “proposed standards and references” in the Supplementary Material of Nosek et al. [] for details). Computational method development and data analyses have become integral to many disciplines, such as biomedical research. For data analyses and software implementations, level 2 of the Nosek et al. Guidelines requires that the code must be posted to a trusted repository. In level 3, they propose the additional requirement that the reported analyzes be reproduced independently before publication. These suggestions overlook the fact that modern biomedical workflows and pipelines consist of multiple applications and libraries, each with their own set of software dependencies. Hence, suites such as Bioconductor [], BioPython [], and BioPerl [] where the user is assured that the dependencies for the components are properly installed have become increasingly popular. The obvious drawback to this approach is that one is limited to the components included in the suite. In addition, reproducing workflows that use interactive graphics remain problematic as each operating system uses their own graphical environment. ![]() Our solution to this problem is GUIdock, which allows for replication of the application, graphics and software environments that produced the analytic results reported in scientific publications. GUIdock uses Docker, an open source project that incorporates a light weight Linux wrapper (container) to ensure application portability and infrastructure flexibility. On a Linux host, Docker uses the host system. On Mac OS and Windows systems, a single Docker container consists of a Virtual Machine (VM) containing the guest software and its Linux environment. Containers differ from traditional VMs in that the resources of the operating system (OS) and not the hardware are shared transparently (virtualized). Multiple containers share a single OS kernel saving considerable resources. Docker also supports Dockerfiles that contain the instructions to build a Docker Image from scratch or another Docker Image. Images can be downloaded from repositories using git or bundled with the Dockerfile to form packages.
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