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the COVID-19 pandemic highlighted the benefits of online training, traditional online tutorials can quickly become outdated and may not cover all the software's functionalities.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.

PLUMED Tutorials: A collaborative, community-driven learning ecosystem / Tribello, Gareth A.; Bonomi, Massimiliano; Bussi, Giovanni; Camilloni, Carlo; Armstrong, Blake I.; Arsiccio, Andrea; Aureli, Simone; Ballabio, Federico; Bernetti, Mattia; Bonati, Luigi; Brookes, Samuel G. H.; Brotzakis, Z. Faidon; Capelli, Riccardo; Ceriotti, Michele; Chan, Kam-Tung; Cossio, Pilar; Dasetty, Siva; Donadio, Davide; Ensing, Bernd; Ferguson, Andrew L.; Fraux, Guillaume; Gale, Julian D.; Gervasio, Francesco Luigi; Giorgino, Toni; Herringer, Nicholas S. M.; Hocky, Glen M.; Hoff, Samuel E.; Invernizzi, Michele; Languin-Cattoën, Olivier; Leone, Vanessa; Limongelli, Vittorio; Lopez-Acevedo, Olga; Marinelli, Fabrizio; Febrer Martinez, Pedro; Masetti, Matteo; Mehdi, Shams; Michaelides, Angelos; Murtada, Mhd Hussein; Parrinello, Michele; Piaggi, Pablo M.; Pietropaolo, Adriana; Pietrucci, Fabio; Pipolo, Silvio; Pritchard, Claire; Raiteri, Paolo; Raniolo, Stefano; Rapetti, Daniele; Rizzi, Valerio; Rydzewski, Jakub; Salvalaglio, Matteo; Schran, Christoph; Seal, Aniruddha; Shayesteh Zadeh, Armin; Silva, Tomás F. D.; Spiwok, Vojtěch; Stirnemann, Guillaume; Sucerquia, Daniel; Tiwary, Pratyush; Valsson, Omar; Vendruscolo, Michele; Voth, Gregory A.; White, Andrew D.; Wu, Jiangbo. - In: THE JOURNAL OF CHEMICAL PHYSICS. - ISSN 0021-9606. - 162:9(2025), pp. 1-27. [10.1063/5.0251501]

PLUMED Tutorials: A collaborative, community-driven learning ecosystem

Tribello, Gareth A.
;
Bonomi, Massimiliano
;
Bussi, Giovanni
;
Bernetti, Mattia;Capelli, Riccardo;Ceriotti, Michele;Cossio, Pilar;Donadio, Davide;Gervasio, Francesco Luigi;Giorgino, Toni;Leone, Vanessa;Marinelli, Fabrizio;Parrinello, Michele;Piaggi, Pablo M.;Pietrucci, Fabio;Rapetti, Daniele;Salvalaglio, Matteo;White, Andrew D.;
2025-01-01

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.
2025
162
9
1
27
092501
https://arxiv.org/abs/2412.03595
Tribello, Gareth A.; Bonomi, Massimiliano; Bussi, Giovanni; Camilloni, Carlo; Armstrong, Blake I.; Arsiccio, Andrea; Aureli, Simone; Ballabio, Federic...espandi
File in questo prodotto:
File Dimensione Formato  
JCP24-SW-PARI2025-05330 (1).pdf

accesso aperto

Tipologia: Documento in Post-print
Licenza: Non specificato
Dimensione 762.01 kB
Formato Adobe PDF
762.01 kB Adobe PDF Visualizza/Apri
092501_1_5.0251501.pdf

embargo fino al 31/03/2026

Tipologia: Versione Editoriale (PDF)
Licenza: Tutti i diritti riservati
Dimensione 7.71 MB
Formato Adobe PDF
7.71 MB Adobe PDF   Visualizza/Apri   Richiedi una copia

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/20.500.11767/145470
Citazioni
  • ???jsp.display-item.citation.pmc??? ND
  • Scopus ND
  • ???jsp.display-item.citation.isi??? 1
social impact