Four simple recommendations to encourage best practices in research software [version 1; referees: 2 approved]

F1000Research

Sonika Tyagi¹  Andrew Treloar²  Petr Holub³  Horst Pichler⁴  Monther Alhamdoosh⁵  David Mellor⁶  Maarten van Gompel⁷  Nicola Mulder⁸  Luis J. Oliveira⁹  Josep Ll. Gelpí^1,10  Daniel S. Katz^1,11  Rob Hooft^1,12  Federico López Gómez^1,13  Martin Cook^1,13  Rafael C. Jiménez^1,13  Robert Pergl^1,14  Björn Grüning^1,15  Bérénice Batut^1,15  Jon Ison^1,16  Harry-Anton Talvik^1,17  Salvador Capella-Gutierrez^1,18  Jonas Hagberg^1,19  Mikael Borg^1,19  Brane Leskošek^2,20  Carole Goble^2,21  Madison Flannery^2,22  Maria V. Schneider^2,22  Simon Gladman^2,22  Philippa C. Griffin^2,22  Bernard Pope^2,22  Daniel Vaughan^2,23  Montserrat González Ferreiro^2,23  Yasset Perez-Riverol^2,23  Leyla Garcia^2,23  Xiaochuan Wang^2,24  Ferran Sanz^2,25  Allegra Via^2,26  Radka Svobodová Vařeková^2,27  Michelle Barker^2,28  Mateusz Kuzak^2,29  Alejandra Gonzalez-Beltran^3,30  Manuel Corpas^3,31  Radosław Suchecki^3,32  Nathan S. Watson-Haigh^3,32  Victoria Stodden^3,33  Ilian Todorov^3,34  Neil Chue Hong^3,35  Steve Crouch^3,36  Rowland Mosbergen^3,37 

[1] Australian Genome Research Facility Ltd., Melbourne, Australia;Australian National Data Service, Melbourne, Australia;BBMRI-ERIC, Neue Stiftingtalstraße 2/B/6, Graz, 8010, Austria;BBMRI.at, Alpen-Adria-University Klagenfurt, Klagenfurt, Austria;CSL Limited, Bio21 Institute, 30 Flemington Road, Parkville, Victoria, 3010, Australia;Center for Open Science, Charlottesville, VA, USA;Centre for Language and Speech Technology, Radboud University Nijmegen, Nijmegen, Netherlands;Computational Biology Division, Department of Integrative Biomedical Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa;DETI/IEETA, University of Aveiro, Aveiro, Portugal;Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, Barcelona, 08028, Spain;Department of Computer Science, University of Illinois Urbana Champaign, Urbana, IL, USA;Dutch TechCenter for Life Sciences and ELIXIR-NL, Utrecht, Netherlands;ELIXIR Hub, Wellcome Genome Campus, Hinxton, CB10 1SD, UK;ELIXIR-CZ, Faculty of Information Technology, Czech Technical University in Prague, Prague, Czech Republic;ELIXIR-DE and de.NBI, Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany;ELIXIR-DK, Technical University of Denmark, Denmark, Denmark;ELIXIR-EE, Institute of Computer Science, University of Tartu, Tartu, Estonia;ELIXIR-ES, Spanish National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Almagro 3, Madrid, 28029, Spain;ELIXIR-SE, National Bioinformatics Infrastructure Sweden (NBIS), Scilifelab, Department of Biochemistry and Biophysics (DBB), Stockholm University, Stockholm, Sweden;ELIXIR-SI, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia;ELIXIR-UK, Software Sustainability Institute, School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK;EMBL Australia Bioinformatics Resource, Lab-14, The University of Melbourne, 700 Swanston St, Parkville, Victoria, 3053, Australia;EMBL-EBI, Wellcome Genome Campus, Hinxton, CB10 1SD, UK;Faculty of Information Technology, Monash University, Victoria, Australia;GRIB, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), Universitat Pompeu Fabra, Barcelona, Spain;IBPM-CNR, Department of Biochemical Sciences , Sapienza University of Rome, Rome, Italy;National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic;National eResearch Collaboration Tools and Resources, Victoria, 3010, Australia;Netherlands eScience Center, Science Park 140, Amsterdam, 1098 XG, Netherlands;Oxford e-Research Centre, University of Oxford, Oxford, UK;Repositive Ltd, Future Business Centre, Cambridge, UK;School of Agriculture, Food & Wine, University of Adelaide, Adelaide, Australia;School of Information Sciences, University of Illinois Urbana Champaign, Urbana, IL, USA;Science & Technologies Facilities Council, Swindon, UK;Software Sustainability Institute, JCMB, University of Edinburgh, Edinburgh, EH9 3FD, UK;Software Sustainability Institute, Web and Internet Science, University of Southampton, Southampton, UK;Stemformatics, University of Melbourne, Melbourne, Australia;

关键词: Bioinformatics;    Data Sharing;   

DOI  :  10.12688/f1000research.11407.1

来源: DOAJ

【 摘 要 】

Scientific research relies on computer software, yet software is not always developed following practices that ensure its quality and sustainability. This manuscript does not aim to propose new software development best practices, but rather to provide simple recommendations that encourage the adoption of existing best practices. Software development best practices promote better quality software, and better quality software improves the reproducibility and reusability of research. These recommendations are designed around Open Source values, and provide practical suggestions that contribute to making research software and its source code more discoverable, reusable and transparent. This manuscript is aimed at developers, but also at organisations, projects, journals and funders that can increase the quality and sustainability of research software by encouraging the adoption of these recommendations.

【 授权许可】

Unknown