Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows.
PLoS Comput Biol
; 20(6): e1012173, 2024 Jun.
Article
in En
| MEDLINE
| ID: mdl-38900779
ABSTRACT
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.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Software
/
Computational Biology
/
Molecular Dynamics Simulation
/
Workflow
Language:
En
Journal:
PLoS Comput Biol
Journal subject:
BIOLOGIA
/
INFORMATICA MEDICA
Year:
2024
Type:
Article
Affiliation country:
Spain