PLUMED Tutorials: A collaborative, community-driven learning ecosystem

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

doi:10.48550/arXiv.2412.03595

PLUMED Tutorials: A collaborative, community-driven learning ecosystem

Gareth A Tribello
, Massimiliano Bonomi
, Giovanni Bussi
, Carlo Camilloni
, Blake I Armstrong
, Andrea Arsiccio
, Simone Aureli
, Federico Ballabio
, Mattia Bernetti
, Luigi Bonati
, Samuel G H Brookes
, Z Faidon Brotzakis
, Riccardo Capelli
, Michele Ceriotti
, Kam-Tung Chan
, Pilar Cossio
, Siva Dasetty
, Davide Donadio
, Bernd Ensing
, Andrew L Ferguson

Guillaume Fraux, Julian D Gale, Francesco Luigi Gervasio, Toni Giorgino, Nicholas S M Herringer, Glen M Hocky, Samuel E Hoff, Michele Invernizzi, Olivier Languin-Cattoën, Vanessa Leone, Vittorio Limongelli, Olga Lopez-Acevedo, Fabrizio Marinelli, Pedro Febrer Martinez, Matteo Masetti, Shams Mehdi, Angelos Michaelides, Mhd Hussein Murtada, Michele Parrinello, Pablo M Piaggi, Adriana Pietropaolo, Fabio Pietrucci, Silvio Pipolo, Claire Pritchard, Paolo Raiteri, Stefano Raniolo, Daniele Rapetti, Valerio Rizzi, Jakub Rydzewski, Matteo Salvalaglio, Christoph Schran, Aniruddha Seal, Armin Shayesteh Zadeh, Tomás F D Silva, Vojtěch Spiwok, Guillaume Stirnemann, Daniel Sucerquia, Pratyush Tiwary, Omar Valsson, Michele Vendruscolo, Gregory A Voth, Andrew D White, Jiangbo Wu

Research output: Contribution to journal › Article › peer-review

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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.

Original language	English
Article number	092501
Journal	Journal of Chemical Physics
Volume	162
Issue number	9
Early online date	04 Mar 2025
DOIs	https://doi.org/10.48550/arXiv.2412.03595 https://doi.org/10.1063/5.0251501
Publication status	Published - 07 Mar 2025

Publications and Copyright Policy

This work is licensed under Queen’s Research Publications and Copyright Policy.

Keywords

Software
COVID-19/epidemiology
Humans

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10.48550/arXiv.2412.03595
10.1063/5.0251501Licence: Unspecified

PLUMED Tutorials: A collaborative, community-driven learning ecosystem
Copyright 2025 the authors. This is an accepted manuscript distributed under a Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited.
Accepted author manuscript, 783 KBLicence: CC BY

Cite this

Tribello, G. A., Bonomi, M., Bussi, G., Camilloni, C., Armstrong, B. I., Arsiccio, A., Aureli, S., Ballabio, F., Bernetti, M., Bonati, L., Brookes, S. G. H., Brotzakis, Z. F., Capelli, R., Ceriotti, M., Chan, K.-T., Cossio, P., Dasetty, S., Donadio, D., Ensing, B., ... Wu, J. (2025). PLUMED Tutorials: A collaborative, community-driven learning ecosystem. Journal of Chemical Physics, 162(9), Article 092501. https://doi.org/10.48550/arXiv.2412.03595, https://doi.org/10.1063/5.0251501

@article{0e45475775f2491faf141636b0cff780,

title = "PLUMED Tutorials: A collaborative, community-driven learning ecosystem",

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{\textquoteright}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.",

keywords = "Software, COVID-19/epidemiology, Humans",

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

year = "2025",

month = mar,

day = "7",

doi = "10.48550/arXiv.2412.03595",

language = "English",

volume = "162",

journal = "Journal of Chemical Physics",

issn = "0021-9606",

publisher = "American Institute of Physics",

number = "9",

}

Tribello, GA, Bonomi, M, Bussi, G, Camilloni, C, Armstrong, BI, Arsiccio, A, Aureli, S, Ballabio, F, Bernetti, M, Bonati, L, Brookes, SGH, Brotzakis, ZF, Capelli, R, Ceriotti, M, Chan, K-T, Cossio, P, Dasetty, S, Donadio, D, Ensing, B, Ferguson, AL, Fraux, G, Gale, JD, Gervasio, FL, Giorgino, T, Herringer, NSM, Hocky, GM, Hoff, SE, Invernizzi, M, Languin-Cattoën, O, Leone, V, Limongelli, V, Lopez-Acevedo, O, Marinelli, F, Febrer Martinez, P, Masetti, M, Mehdi, S, Michaelides, A, Murtada, MH, Parrinello, M, Piaggi, PM, Pietropaolo, A, Pietrucci, F, Pipolo, S, Pritchard, C, Raiteri, P, Raniolo, S, Rapetti, D, Rizzi, V, Rydzewski, J, Salvalaglio, M, Schran, C, Seal, A, Shayesteh Zadeh, A, Silva, TFD, Spiwok, V, Stirnemann, G, Sucerquia, D, Tiwary, P, Valsson, O, Vendruscolo, M, Voth, GA, White, AD & Wu, J 2025, 'PLUMED Tutorials: A collaborative, community-driven learning ecosystem', Journal of Chemical Physics, vol. 162, no. 9, 092501. https://doi.org/10.48550/arXiv.2412.03595, https://doi.org/10.1063/5.0251501

TY - JOUR

T1 - PLUMED Tutorials: A collaborative, community-driven learning ecosystem

AU - Tribello, Gareth A

AU - Bonomi, Massimiliano

AU - Bussi, Giovanni

AU - Camilloni, Carlo

AU - Armstrong, Blake I

AU - Arsiccio, Andrea

AU - Aureli, Simone

AU - Ballabio, Federico

AU - Bernetti, Mattia

AU - Bonati, Luigi

AU - Brookes, Samuel G H

AU - Brotzakis, Z Faidon

AU - Capelli, Riccardo

AU - Ceriotti, Michele

AU - Chan, Kam-Tung

AU - Cossio, Pilar

AU - Dasetty, Siva

AU - Donadio, Davide

AU - Ensing, Bernd

AU - Ferguson, Andrew L

AU - Fraux, Guillaume

AU - Gale, Julian D

AU - Gervasio, Francesco Luigi

AU - Giorgino, Toni

AU - Herringer, Nicholas S M

AU - Hocky, Glen M

AU - Hoff, Samuel E

AU - Invernizzi, Michele

AU - Languin-Cattoën, Olivier

AU - Leone, Vanessa

AU - Limongelli, Vittorio

AU - Lopez-Acevedo, Olga

AU - Marinelli, Fabrizio

AU - Febrer Martinez, Pedro

AU - Masetti, Matteo

AU - Mehdi, Shams

AU - Michaelides, Angelos

AU - Murtada, Mhd Hussein

AU - Parrinello, Michele

AU - Piaggi, Pablo M

AU - Pietropaolo, Adriana

AU - Pietrucci, Fabio

AU - Pipolo, Silvio

AU - Pritchard, Claire

AU - Raiteri, Paolo

AU - Raniolo, Stefano

AU - Rapetti, Daniele

AU - Rizzi, Valerio

AU - Rydzewski, Jakub

AU - Salvalaglio, Matteo

AU - Schran, Christoph

AU - Seal, Aniruddha

AU - Shayesteh Zadeh, Armin

AU - Silva, Tomás F D

AU - Spiwok, Vojtěch

AU - Stirnemann, Guillaume

AU - Sucerquia, Daniel

AU - Tiwary, Pratyush

AU - Valsson, Omar

AU - Vendruscolo, Michele

AU - Voth, Gregory A

AU - White, Andrew D

AU - Wu, Jiangbo

PY - 2025/3/7

Y1 - 2025/3/7

N2 - 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.

AB - 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.

KW - Software

KW - COVID-19/epidemiology

KW - Humans

U2 - 10.48550/arXiv.2412.03595

DO - 10.48550/arXiv.2412.03595

M3 - Article

C2 - 40035582

SN - 0021-9606

VL - 162

JO - Journal of Chemical Physics

JF - Journal of Chemical Physics

IS - 9

M1 - 092501

ER -

PLUMED Tutorials: A collaborative, community-driven learning ecosystem

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