PLUMED Tutorials: A collaborative, community-driven learning ecosystem

In computational physics, chemistry, and biology, the implementation of new techniques in shared and open-source software lowers barriers to entry and promotes rapid scientific progress. However, effectively training new software users presents several challenges. Common methods like direct knowledge transfer and in-person workshops are limited in reach and comprehensiveness. Furthermore, while the COVID-19 pandemic highlighted the benefits of online training, traditional online tutorials can quickly become outdated and may not cover all the software's functionalities. To address these issues, here we introduce "PLUMED Tutorials," a collaborative model for developing, sharing, and updating online tutorials. This initiative utilizes repository management and continuous integration to ensure compatibility with software updates. Moreover, the tutorials are interconnected to form a structured learning path and are enriched with automatic annotations to provide broader context. This paper illustrates the development, features, and advantages of PLUMED Tutorials, aiming to foster an open community for creating and sharing educational resources.

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Publication Details

Journal
The Journal of Chemical Physics
Published
2025-03-04
DOI
https://doi.org/10.1063/5.0251501
Citations
26
Primary Topic
Scientific Computing and Data Management
Type
article
Field-Weighted Citation Impact
108.39

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article

PLUMED Tutorials: A collaborative, community-driven learning ecosystem

Simone Aureli, Jakub Rydzewski, Giovanni Bussi, Stefano Raniolo et al.
26 citations
The Journal of Chemical Physics
Scientific Computing and Data Management
108.39
article

PLUMED Tutorials: A collaborative, community-driven learning ecosystem

Simone Aureli, Jakub Rydzewski, Giovanni Bussi, Stefano Raniolo, Gareth A. Tribello, Aniruddha Seal, Michele Invernizzi, Davide Donadio, Guillaume Fraux, Fabio Pietrucci, Nicholas S. M. Herringer, Jiangbo Wu, Julian D. Gale, Michele Ceriotti, Olga Lopez‐Acevedo, Francesco Luigi Gervasio, Andrew L. Ferguson, Michele Parrinello, Vittorio Limongelli, Christoph Schran, Andrea Arsiccio, Blake Armstrong, Daniele Rapetti, Z. Faidon Brotzakis, Michele Vendruscolo, Matteo Masetti, Riccardo Capelli, Adriana Pietropaolo, Kam-Tung Chan, Carlo Camilloni, Vanessa Leone, Christopher Pritchard, Matteo Salvalaglio, Tomás F. D. Silva, Ómar Valsson, Toni Giorgino, Daniel Sucerquia, Mhd Hussein Murtada, Massimiliano Bonomi, Angelos Michaelides, Samuel E. Hoff, Armin Shayesteh Zadeh, Pilar Cossio, Fabrizio Marinelli, Vojtěch Spiwok, Pratyush Tiwary, Paolo Raiteri, Guillaume Stirnemann, Pablo M. Piaggi, Shams Mehdi, Federico Ballabio, Mattia Bernetti, Valerio Rizzi, Olivier Languin–Cattoën, Samuel G. H. Brookes, Glen M. Hocky, Gregory A. Voth, Siva Dasetty, Luigi Bonati, Silvio Pipolo, Bernd Ensing, Andrew Dickson White, Pedro Febrer Martinez
article en
26 citations

Abstract

In computational physics, chemistry, and biology, the implementation of new techniques in shared and open-source software lowers barriers to entry and promotes rapid scientific progress. However, effectively training new software users presents several challenges. Common methods like direct knowledge transfer and in-person workshops are limited in reach and comprehensiveness. Furthermore, while the COVID-19 pandemic highlighted the benefits of online training, traditional online tutorials can quickly become outdated and may not cover all the software's functionalities. To address these issues, here we introduce "PLUMED Tutorials," a collaborative model for developing, sharing, and updating online tutorials. This initiative utilizes repository management and continuous integration to ensure compatibility with software updates. Moreover, the tutorials are interconnected to form a structured learning path and are enriched with automatic annotations to provide broader context. This paper illustrates the development, features, and advantages of PLUMED Tutorials, aiming to foster an open community for creating and sharing educational resources.

The Journal of Chemical PhysicsVol. 162(9)
Ikerbasque (ES), University of Geneva (CH), University of North Texas (US), Queen's University Belfast (GB), SIB Swiss Institute of Bioinformatics (CH), Centre National de la Recherche Scientifique (FR), Centrum Wiskunde & Informatica (NL), Scuola Internazionale Superiore di Studi Avanzati (IT), Institut Pasteur (FR), Chicago Institute for Psychoanalysis (US), University of Milan (IT), University of Urbino (IT), Medical College of Wisconsin (US), Université Paris Cité (FR), Université de Lille (FR), University of Cambridge (GB), Université Paris Sciences et Lettres (FR), École Normale Supérieure - PSL (FR), Nicolaus Copernicus University (PL), Italian Institute of Technology (IT), Thomas Young Centre (GB), Universidad de Antioquia (CO), Magna Graecia University (IT), Sorbonne Université (FR), University of Chicago (US), CIC nanoGUNE (ES), FZU ‒ Institute of Physics of the Academy of Sciences of the Czech Republic (CZ), Instituto di Biofisica (ES), Institut de minéralogie, de physique des matériaux et de cosmochimie (FR), Flatiron Health (United States) (US), National Research Council (IT), Université d'Artois (FR), University College London (GB), École Polytechnique Fédérale de Lausanne (CH), University of Rochester (US), Università della Svizzera italiana (CH), New York University (US), University of Maryland, College Park (US), Alexander Fleming Biomedical Sciences Research Center (GR), Heidelberg Institute for Theoretical Studies (DE), University of California, Davis (US), University of Amsterdam (NL), University of Chemistry and Technology, Prague (CZ), University of Bologna (IT)
National Science Foundation, U.S. Department of Energy, European Molecular Biology Organization, Royal Society, European Commission, Agence Nationale de la Recherche, Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, Horizon 2020 Framework Programme, Engineering and Physical Sciences Research Council, Australian Research Council, HORIZON EUROPE Marie Sklodowska-Curie Actions
Openalex Percentile: Top 0%
Scientific Computing and Data Management
108.39
DOIOpen Access PDFOpenAlex
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