Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows.

Autor: Genís Bayarri, Pau Andrio, Josep Lluís Gelpí, Adam Hospital, Modesto Orozco
Jazyk: angličtina
Rok vydání: 2024
Předmět:
Zdroj: PLoS Computational Biology, Vol 20, Iss 6, p e1012173 (2024)
Druh dokumentu: article
ISSN: 1553-734X
1553-7358
DOI: 10.1371/journal.pcbi.1012173
Popis: Interactive Jupyter Notebooks in combination with Conda environments can be used to generate FAIR (Findable, Accessible, Interoperable and Reusable/Reproducible) biomolecular simulation workflows. The interactive programming code accompanied by documentation and the possibility to inspect intermediate results with versatile graphical charts and data visualization is very helpful, especially in iterative processes, where parameters might be adjusted to a particular system of interest. This work presents a collection of FAIR notebooks covering various areas of the biomolecular simulation field, such as molecular dynamics (MD), protein-ligand docking, molecular checking/modeling, molecular interactions, and free energy perturbations. Workflows can be launched with myBinder or easily installed in a local system. The collection of notebooks aims to provide a compilation of demonstration workflows, and it is continuously updated and expanded with examples using new methodologies and tools.
Databáze: Directory of Open Access Journals
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