Stian Soiland-Reyes

A microscopic slide, herbarium specimen and pinned insect, with old annotated labels.

The Specimen Data Refinery: A Canonical Workflow Framework and FAIR Digital Object Approach to Speeding up Digital Mobilisation of Natural History Collections

April 1, 2022May 16, 2022Stian Soiland-Reyes

A key limiting factor in organising and using information from physical specimens curated in natural science collections is making that information computable, with [...]

BioExcel Whitepaper on Scientific Software Development (BioExcel-2 update)

March 31, 2022June 22, 2022Stian Soiland-Reyes

This white paper presents the experience of the developers and recommendations for development of high-quality software engineering processes. [...]

20,000 jobs of GROMACS simulation ensemble to HyperBatch global job distribution. Compute instances distributed globally as Intel, AMD, ARM, GPU

GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design

March 30, 2022May 16, 2022Stian Soiland-Reyes

We assess costs and efficiency of state-of-the-art high-performance cloud computing and compare the results to traditional on-premises compute clusters. Our use case is [...]

Ten Simple Rules for making a software tool workflow-ready

March 24, 2022June 22, 2022Stian Soiland-Reyes

There is little specific guidance for writing software intended to slot in as a tool within a workflow; or on converting an existing standalone research-quality software tool into a reusable, composable, well-behaved citizen within a larger workflow. In this paper we present 10 simple rules for how a software tool can be prepared for workflow use [...]

Main conformational states, overall tetrameric structure, and RTG binding site of the KCNQ2 channel

Molecular Insights Into Binding and Activation of the Human KCNQ2 Channel by Retigabine

March 16, 2022May 16, 2022Stian Soiland-Reyes

Voltage-gated potassium channels of the Kv7.x family are involved in a plethora of biological processes across many tissues in animals, and their misfunctioning [...]

Making Canonical Workflow Building Blocks interoperable across workflow languages

March 7, 2022May 16, 2022Stian Soiland-Reyes

We introduce the concept of Canonical Workflow Building Blocks (CWBB), a methodology of describing and wrapping computational tools, in order for them to be utilised in a reproducible manner from multiple workflow languages and execution platforms. [...]

BioExcel – Centre of Excellence for Computation Biomolecular Research

Centre of Excellence for Computational Biomolecular Research

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Stian Soiland-Reyes