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the COVID-19 pandemic highlighted the benefits of online training, traditional online tutorials can quickly become outdated and may not cover all the software’s functionalities.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.
Article Details
Journal Info
The Journal of Chemical Physics
American Institute of Physics
Authors (63)
Gareth A. Tribello
Centre for Quantum Materials and Technologies, School of Mathematics and Physics, Queen's University Belfast 1 , Belfast,
Massimiliano Bonomi
Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Computational Structural Biology Unit 2 , Paris,
Giovanni Bussi
Molecular and Statistical Biophysics
Carlo Camilloni
Department of Biosciences, University of Milano 4 , Milano,
Blake I. Armstrong
School of Molecular and Life Sciences 1 , Perth, Western Australia,
Andrea Arsiccio
Coriolis Pharma 6 , Fraunhoferstrasse 18b, 82152 Martinsried,
Simone Aureli
School of Pharmaceutical Sciences, University of Geneva 1 , Rue Michel-Servet 1, 1206 Genève,
Federico Ballabio
Department of Biosciences, University of Milano 4 , Milano,
Mattia Bernetti
Department of Biomolecular Sciences, University of Urbino “Carlo Bo 11 ,” Piazza Rinascimento 6, 61029 Urbino,
Luigi Bonati
Atomistic Simulations, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16142 Genoa, Italy
Samuel G. H. Brookes
Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
Z. Faidon Brotzakis
Riccardo Capelli
Department of Biosciences, Università degli Studi di Milano , Via Celoria 26, 20133 Milan,
Michele Ceriotti
Laboratory of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne 1 , 1015 Lausanne,
Kam-Tung Chan
Department of Chemistry, University of California 1 , Davis, California 95616,
Pilar Cossio
Center for Computational Mathematics
Siva Dasetty
Pritzker School of Molecular Engineering, University of Chicago 21 , Chicago, Illinois 60637,
Davide Donadio
Department of Chemistry
Bernd Ensing
Computational Chemistry, Van ’t Hoff Institute for Molecular Sciences and Amsterdam Center for Multiscale Modeling, University of Amsterdam 1 , Science Park 904, 1098 XH Amsterdam,
Andrew L. Ferguson
Department of Chemistry
Guillaume Fraux
Laboratory of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne , 1015 Lausanne,
Julian D. Gale
School of Molecular and Life Sciences
Francesco Luigi Gervasio
Department of Pharmaceutical Sciences
Toni Giorgino
National Research Council of Italy, Biophysics Institute (CNR-IBF) 10 , Via Celoria 26, Milan 20133,
Nicholas S. M. Herringer
Department of Chemistry, University of Chicago 24 , Chicago, Illinois 60637,
Glen M. Hocky
Department of Chemistry
Samuel E. Hoff
Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Computational Structural Biology Unit 2 , Paris,
Michele Invernizzi
Peptone Ltd. 27 , The Connolly Works 41-43, Chalton Street, London NW1 1JD,
Olivier Languin-Cattoën
Scuola Internazionale Superiore di Studi Avanzati (SISSA) 3 , Via Bonomea 265, 34136 Trieste,
Vanessa Leone
Department of Biophysics and Data Science Institute, Medical College of Wisconsin 28 , Milwaukee, Wisconsin 53226-3548,
Vittorio Limongelli
Olga Lopez-Acevedo
Biophysics of Tropical Diseases Max Planck Tandem Group, University of Antioquia UdeA 30 , 050010 Medellin,
Fabrizio Marinelli
Department of Biophysics and Data Science Institute, Medical College of Wisconsin 28 , Milwaukee, Wisconsin 53226-3548,
Pedro Febrer Martinez
School of Pharmaceutical Sciences, University of Geneva 7 , Rue Michel-Servet 1, CH-1206 Geneva,
Matteo Masetti
Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna 12 , Via Belmeloro 6, 40126 Bologna,
Shams Mehdi
Department of Chemistry and Biochemistry, Institute for Physical Science and Technology, University of Maryland 31 , College Park, Maryland 20742,
Angelos Michaelides
Mhd Hussein Murtada
Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge 32 , Cambridge,
Michele Parrinello
Atomistic Simulations, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16142 Genoa, Italy
Pablo M. Piaggi
CIC nanoGUNE BRTA
Adriana Pietropaolo
Dipartimento di Scienze della Salute, Università Magna Graecia di Catanzaro 34 , Viale Europa, 88100 Catanzaro,
Fabio Pietrucci
Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 CNRS, Sorbonne Université, Muséum National d’Histoire Naturelle 35 , Paris 75005,
Silvio Pipolo
UCCS Unité de Catalyse et Chimie du Solide, Université de Lille, Université d’Artois UMR 8181 36 , F-59000 Lille,
Claire Pritchard
PASTEUR, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS 37 , 24 rue Lhomond, 75005 Paris,
Paolo Raiteri
School of Molecular and Life Sciences
Stefano Raniolo
Euler Institute, Faculty of Biomedical Sciences, Universitá della Svizzera italiana (USI) , via G. Buffi 13, CH-6900 Lugano,
Daniele Rapetti
Department of Applied Science and Technology, Politecnico di Torino , Corso Duca degli Abruzzi 24, 10129 Torino,
Valerio Rizzi
School of Pharmaceutical Sciences, University of Geneva 1 , Rue Michel-Servet 1, 1206 Genève,
Jakub Rydzewski
Faculty of Physics, Astronomy and Informatics, Institute of Physics, Nicolaus Copernicus University 38 , Grudziadzka 5, 87-100 Toruń,
Matteo Salvalaglio
Department of Chemical Engineering
Christoph Schran
Aniruddha Seal
Department of Chemistry and Chicago Center for Theoretical Chemistry
Armin Shayesteh Zadeh
Pritzker School of Molecular Engineering, University of Chicago 21 , Chicago, Illinois 60637,
Tomás F. D. Silva
Scuola Internazionale Superiore di Studi Avanzati (SISSA) 3 , Via Bonomea 265, 34136 Trieste,
Vojtěch Spiwok
Department of Biochemistry and Microbiology–University of Chemistry and Technology 1 , Prague,
Guillaume Stirnemann
CPCV, Département de Chimie
Daniel Sucerquia
Heidelberg Institute for Theoretical Studies 1 , Heidelberg 69118,
Pratyush Tiwary
Omar Valsson
Department of Chemistry
Michele Vendruscolo
Gregory A. Voth
Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics
Andrew D. White
Jiangbo Wu
Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago