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.
Highlights d An open-source graphical tool for constructing and executing bioinformatics workflows d Uses Docker containers to ensure reproducibility and facilitate workflow installation d Interactive graphical modules such as Jupyter and Cytoscape are supported d Workflows can be saved in Bwb's native format or exported as portable shell scripts
We present BioDepot-workflow-Builder (BwB), a portable and open-source tool for creating bioinformatics workflows with a simple drag-and-drop graphical user interface. The individual components of the workflows are Docker containers which are available from public repositories or provided by the user. The use of software containers ensures that workflows will give identical results across different operating systems and hardware architectures. The use of Docker also allows for individual components to be deployed on the cloud. The modularity and ease of customization and installation of bioinformatics tools using BwB allows for researchers to efficiently test new workflows and compare competing algorithms. Since BwB itself is packaged in a Docker container, the setup is minimal. In particular, users only need to install Docker and have access to a web browser to begin creating and running workflows. As a proof-of-concept case study, we illustrated the feasibility of BwB by developing widgets for the RNA-seq differential expression analysis workflow employed by the NIH BD2K-LINCS Drug Toxicity Signature Generation Center at Mount Sinai. The app and all the containers are available on the BioDepot repository (https://hub.docker.com/r/biodepot).
Background: Software container technology such as Docker can be used to package and distribute bioinformatics workflows consisting of multiple software implementations and dependencies. However, Docker is a command line–based tool, and many bioinformatics pipelines consist of components that require a graphical user interface. Results: We present a container tool called GUIdock-VNC that uses a graphical desktop sharing system to provide a browser-based interface for containerized software. GUIdock-VNC uses the Virtual Network Computing protocol to render the graphics within most commonly used browsers. We also present a minimal image builder that can add our proposed graphical desktop sharing system to any Docker packages, with the end result that any Docker packages can be run using a graphical desktop within a browser. In addition, GUIdock-VNC uses the Oauth2 authentication protocols when deployed on the cloud. Conclusions: As a proof-of-concept, we demonstrated the utility of GUIdock-noVNC in gene network inference. We benchmarked our container implementation on various operating systems and showed that our solution creates minimal overhead.
Prostate cancer is the most common cancer among men in developed countries. Androgen deprivation therapy (ADT) is the standard treatment for prostate cancer. However, approximately one third of all patients with metastatic disease treated with ADT develop resistance to ADT. This condition is called metastatic castrate-resistant prostate cancer (mCRPC). Patients who do not respond to hormone therapy are often treated with a chemotherapy drug called docetaxel. Sub-challenge 2 of the Prostate Cancer DREAM Challenge aims to improve the prediction of whether a patient with mCRPC would discontinue docetaxel treatment due to adverse effects. Specifically, a dataset containing three distinct clinical studies of patients with mCRPC treated with docetaxel was provided. We applied the k-nearest neighbor method for missing data imputation, the hill climbing algorithm and random forest importance for feature selection, and the random forest algorithm for classification. We also empirically studied the performance of many classification algorithms, including support vector machines and neural networks. Additionally, we found using random forest importance for feature selection provided slightly better results than the more computationally expensive method of hill climbing.
UUPK memberikan dua pilihan penyelesaian sengketa kepada konsumen dan pelaku usaha yaitu penyelesaian sengketa di luar pengadilan melalui BPSK atau melalui Pengadilan. BPSK memiliki kewenangan mengeluarkan suatu putusan yang sifat putusannya adalah final dan mengikat. Dari hal ini kemudian muncul suatu isu hukum apakah putusan BPSK yang final dan mengikat sama artinya dengan final dan mengikat pada putusan pengadilan atau memiliki makna yang berbeda. Penulis beragumen bahwa kedua putusan tersebut di atas bukan merupakan hal yang sama. Hal ini karena atas putusan BPSK masih dapat dilakukan upaya hukum lebih lanjut ke Pengadilan. Penelitian ini adalah penelitian hukum dengan menggunakan pendekatan perundang-undangan dan pendekatan komparatif. Consumer Protection Law provides two alternatives for dispute resolution to consumers and businessmen. The alternatives are outside the court through the Consumer Dispute Settlement Agency (BPSK) and the Court. BPSK has the authority to make a decision that is final and binding. This feature raises a legal question on whether the final and binding decision issued by BPSK has the same meaning as the Court’s decision. The author argues that those decisions are typically different because, on BPSK’s decision, an appeal could be made to the Court. This article is legal research that uses a statute approach and comparative approach.
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