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Related Experiment Video

Updated: Mar 12, 2026

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

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Published on: May 9, 2017

Bringing your tools to CyVerse Discovery Environment using Docker.

Upendra Kumar Devisetty¹, Kathleen Kennedy¹, Paul Sarando¹

¹CyVerse, University of Arizona, Tucson, AR, 85721, USA.

|November 3, 2016

Summary

This summary is machine-generated.

Docker containerization simplifies scientific software deployment, enabling platform independence and reproducibility. This facilitates easier integration and sharing of tools within environments like CyVerse Discovery Environment.

Keywords:

CyVerse Discovery Environment virtualization platform

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Published on: December 7, 2021

Area of Science:

Computational Science
Bioinformatics
Software Engineering

Background:

Docker containerization offers a standardized method for packaging and distributing scientific software and its dependencies.
Traditional scientific software installation is often complex, time-consuming, and prone to environment-specific issues.
Reproducibility and platform independence are critical challenges in scientific computing.

Purpose of the Study:

To demonstrate how Docker can streamline the integration of scientific tools into the CyVerse Discovery Environment (DE).
To provide a method for users to easily deploy their own software stacks within a cloud-based research environment.
To facilitate the sharing and public release of scientific applications.

Main Methods:

Utilizing Docker to create containerized scientific software environments.
Integrating these Docker containers into the CyVerse Discovery Environment for deployment.
Leveraging Docker's capabilities for versioning and reproducibility of software stacks.

Main Results:

Docker enables one-time installation of complex scientific software, eliminating repetitive setup.
Platform-independent deployment of identical software stacks across diverse computing environments (e.g., XSEDE, AWS).
Simplified tool integration into CyVerse DE, enhancing ease of use compared to previous methods.

Conclusions:

Docker significantly simplifies the packaging, distribution, and deployment of scientific software.
The CyVerse Discovery Environment effectively utilizes Docker for integrating and delivering community software tools.
This approach empowers researchers to easily share their applications and collaborate more effectively.