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BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows.

Pau Andrio1, Adam Hospital2, Javier Conejero1

  • 1Barcelona Supercomputing Center (BSC), Jordi Girona 29, 08034, Barcelona, Spain.

Scientific Data
|September 12, 2019
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Summary
This summary is machine-generated.

Biomolecular simulations are now more integrated with bioinformatics workflows. The new BioExcel Building Blocks (BioBB) library offers interoperable Python wrappers for easier use in computational environments.

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Area of Science:

  • Computational Biology
  • Bioinformatics

Background:

  • Biomolecular simulations are powerful tools for studying biological processes, benefiting from advances in software and hardware.
  • Current simulation software lacks integration with standard bioinformatics technologies like automated deployment and workflow orchestration.
  • This hinders the adoption of modern computational practices in biomolecular simulation research.

Purpose of the Study:

  • To integrate biomolecular simulations with established bioinformatics workflows.
  • To develop a library that facilitates the adoption of modern software engineering practices in the field.
  • To enhance the usability and interoperability of biomolecular simulation tools.

Main Methods:

  • Development of the BioExcel Building Blocks (BioBB) library, featuring Python wrappers for interoperability.
  • Integration of BioBBs with standard software management tools for automated processes.
  • Creation of data ontologies, documentation, and software containers for BioBBs.

Main Results:

  • The BioBB library provides an interoperable architecture for biomolecular simulations.
  • BioBBs have been successfully integrated into automated deployment systems and workflow managers.
  • The library supports the generation of data ontologies, documentation, and software containers.

Conclusions:

  • The BioBB library successfully bridges the gap between biomolecular simulations and the bioinformatics community's working methods.
  • This integration enhances the usability of biomolecular simulations across diverse computational environments.
  • The developed tools promote wider adoption of automated and containerized solutions in the field.