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BioExcel-2 Deliverable 2.6 – Integration of BioExcel software framework with standards and international initiatives

Authors: Stian Soiland-Reyes; Adam Hospital; Genís Bayarri; Ania Niewelska; Cibin Sadasivan Baby; Douglas Lowe; Pau Andrio; +1 Authors

BioExcel-2 Deliverable 2.6 – Integration of BioExcel software framework with standards and international initiatives

Abstract

This deliverable details the integration of the BioExcel computational framework with external initiatives and standards for the purpose of interoperability and portability, as well as wider FAIR aspects on discoverability and metadata. An ongoing challenge for users to take advantage of BioExcel tools in workflow management systems and across multiple compute infrastructures is to get the software installed and integrated into their system, without losing the significant optimization performance gains developed by BioExcel. Our work on forming the BioExcel Building Blocks (BioBB) have helped unify programmatic invocation of biomolecular simulation and modelling tools, making it easier to include them in major workflow systems in life sciences. Technically the building block functionality has been made possibly by building on multiple standards, technologies and initiatives for interoperability, as detailed in this deliverable. This document expands on how we have addressed Exascale challenges such as supporting multiple hardware-optimized binaries for execution on a variety of cloud compute environments. This is significant because the compute landscape has changed for BioExcel users towards a hybrid model of private clusters and public cloud usage. Workflows, which capture a computational method for reuse, need to be portable not just across these compute backends but also between different workflow systems. This is important to reliably apply a workflow through a wide range of scenarios: from training and prototyping, through development and customization towards scalable production runs. We have identified and generalized another advantage of what we call canonical workflow building blocks, that a conceptual workflow using a combination of blocks can be realized the same way in multiple workflow systems and give reproducible results, thanks to their common behaviour and underlying software packaging mechanisms. We show how our active engagement with ongoing initiatives have influenced WP2 development, publication of workflows and the BioExcel Building Blocks, as well as further evolved the standards themselves.

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
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