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Related Experiment Video

Updated: Jun 12, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Opal web services for biomedical applications.

Jingyuan Ren1, Nadya Williams, Luca Clementi

  • 1National Biomedical Computation Resource, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. j2ren@ucsd.edu

Nucleic Acids Research
|June 10, 2010
PubMed
Summary
This summary is machine-generated.

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Scientific Software as a Service (sSaaS) provides scalable access to complex biomedical applications via web interfaces. This approach, powered by the Opal toolkit, simplifies deployment and has successfully executed over 239,000 jobs.

Area of Science:

  • Biomedical Informatics
  • Computational Biology
  • High-Performance Computing

Background:

  • Biomedical research increasingly demands high-performance computing resources due to application complexity.
  • Traditional deployment methods are challenged by advances in cluster, grid, and cloud computing.
  • New support models are needed for efficient biomedical research workflows.

Purpose of the Study:

  • To develop a scalable and transparent access model for complex biomedical applications.
  • To facilitate the integration of scientific software into research workflows.
  • To provide a robust platform for executing computational biology tasks.

Main Methods:

  • Implemented Scientific Software as a Service (sSaaS) using the Opal toolkit.

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Published on: September 22, 2021

Related Experiment Videos

Last Updated: Jun 12, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Establishing an Octopus Ecosystem for Biomedical and Bioengineering Research
09:10

Establishing an Octopus Ecosystem for Biomedical and Bioengineering Research

Published on: September 22, 2021

  • Wrapped scientific applications (e.g., MEME, AutoDock, APBS) as web services without code modification.
  • Enabled both web form-based and programmatic access to applications via SOAP and workflow tools.

    • Main Results:

    • Launched a production web server (ws.nbcr.net) in 2007, now supporting multiple bioinformatics and computational biology tools.
    • Successfully executed 239,814 jobs between August 2007 and December 2009.
    • Observed a daily job execution rate more than doubling from 2008 to 2009.

    Conclusions:

    • The Opal-enabled sSaaS model effectively supports diverse biomedical applications.
    • This service model enhances interoperation between scientific applications.
    • It allows researchers to focus on scientific discovery and workflow development rather than infrastructure management.