F1000Research (Jun 2017)
Four simple recommendations to encourage best practices in research software [version 1; referees: 2 approved]
- Rafael C. Jiménez,
- Mateusz Kuzak,
- Monther Alhamdoosh,
- Michelle Barker,
- Bérénice Batut,
- Mikael Borg,
- Salvador Capella-Gutierrez,
- Neil Chue Hong,
- Martin Cook,
- Manuel Corpas,
- Madison Flannery,
- Leyla Garcia,
- Josep Ll. Gelpí,
- Simon Gladman,
- Carole Goble,
- Montserrat González Ferreiro,
- Alejandra Gonzalez-Beltran,
- Philippa C. Griffin,
- Björn Grüning,
- Jonas Hagberg,
- Petr Holub,
- Rob Hooft,
- Jon Ison,
- Daniel S. Katz,
- Brane Leskošek,
- Federico López Gómez,
- Luis J. Oliveira,
- David Mellor,
- Rowland Mosbergen,
- Nicola Mulder,
- Yasset Perez-Riverol,
- Robert Pergl,
- Horst Pichler,
- Bernard Pope,
- Ferran Sanz,
- Maria V. Schneider,
- Victoria Stodden,
- Radosław Suchecki,
- Radka Svobodová Vařeková,
- Harry-Anton Talvik,
- Ilian Todorov,
- Andrew Treloar,
- Sonika Tyagi,
- Maarten van Gompel,
- Daniel Vaughan,
- Allegra Via,
- Xiaochuan Wang,
- Nathan S. Watson-Haigh,
- Steve Crouch
Affiliations
- Rafael C. Jiménez
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
- Mateusz Kuzak
- Netherlands eScience Center, Science Park 140, Amsterdam, 1098 XG, Netherlands
- Monther Alhamdoosh
- CSL Limited, Bio21 Institute, 30 Flemington Road, Parkville, Victoria, 3010, Australia
- Michelle Barker
- National eResearch Collaboration Tools and Resources, Victoria, 3010, Australia
- Bérénice Batut
- ELIXIR-DE and de.NBI, Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
- Mikael Borg
- ELIXIR-SE, National Bioinformatics Infrastructure Sweden (NBIS), Scilifelab, Department of Biochemistry and Biophysics (DBB), Stockholm University, Stockholm, Sweden
- Salvador Capella-Gutierrez
- ELIXIR-ES, Spanish National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Almagro 3, Madrid, 28029, Spain
- Neil Chue Hong
- Software Sustainability Institute, JCMB, University of Edinburgh, Edinburgh, EH9 3FD, UK
- Martin Cook
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
- Manuel Corpas
- Repositive Ltd, Future Business Centre, Cambridge, UK
- Madison Flannery
- EMBL Australia Bioinformatics Resource, Lab-14, The University of Melbourne, 700 Swanston St, Parkville, Victoria, 3053, Australia
- Leyla Garcia
- EMBL-EBI, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
- Josep Ll. Gelpí
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, Barcelona, 08028, Spain
- Simon Gladman
- EMBL Australia Bioinformatics Resource, Lab-14, The University of Melbourne, 700 Swanston St, Parkville, Victoria, 3053, Australia
- Carole Goble
- ELIXIR-UK, Software Sustainability Institute, School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
- Montserrat González Ferreiro
- EMBL-EBI, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
- Alejandra Gonzalez-Beltran
- Oxford e-Research Centre, University of Oxford, Oxford, UK
- Philippa C. Griffin
- EMBL Australia Bioinformatics Resource, Lab-14, The University of Melbourne, 700 Swanston St, Parkville, Victoria, 3053, Australia
- Björn Grüning
- ELIXIR-DE and de.NBI, Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
- Jonas Hagberg
- ELIXIR-SE, National Bioinformatics Infrastructure Sweden (NBIS), Scilifelab, Department of Biochemistry and Biophysics (DBB), Stockholm University, Stockholm, Sweden
- Petr Holub
- BBMRI-ERIC, Neue Stiftingtalstraße 2/B/6, Graz, 8010, Austria
- Rob Hooft
- Dutch TechCenter for Life Sciences and ELIXIR-NL, Utrecht, Netherlands
- Jon Ison
- ELIXIR-DK, Technical University of Denmark, Denmark, Denmark
- Daniel S. Katz
- Department of Computer Science, University of Illinois Urbana Champaign, Urbana, IL, USA
- Brane Leskošek
- ELIXIR-SI, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Federico López Gómez
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
- Luis J. Oliveira
- DETI/IEETA, University of Aveiro, Aveiro, Portugal
- David Mellor
- Center for Open Science, Charlottesville, VA, USA
- Rowland Mosbergen
- Stemformatics, University of Melbourne, Melbourne, Australia
- Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Yasset Perez-Riverol
- EMBL-EBI, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
- Robert Pergl
- ELIXIR-CZ, Faculty of Information Technology, Czech Technical University in Prague, Prague, Czech Republic
- Horst Pichler
- BBMRI.at, Alpen-Adria-University Klagenfurt, Klagenfurt, Austria
- Bernard Pope
- EMBL Australia Bioinformatics Resource, Lab-14, The University of Melbourne, 700 Swanston St, Parkville, Victoria, 3053, Australia
- Ferran Sanz
- GRIB, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), Universitat Pompeu Fabra, Barcelona, Spain
- Maria V. Schneider
- EMBL Australia Bioinformatics Resource, Lab-14, The University of Melbourne, 700 Swanston St, Parkville, Victoria, 3053, Australia
- Victoria Stodden
- School of Information Sciences, University of Illinois Urbana Champaign, Urbana, IL, USA
- Radosław Suchecki
- School of Agriculture, Food & Wine, University of Adelaide, Adelaide, Australia
- Radka Svobodová Vařeková
- National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
- Harry-Anton Talvik
- ELIXIR-EE, Institute of Computer Science, University of Tartu, Tartu, Estonia
- Ilian Todorov
- Science & Technologies Facilities Council, Swindon, UK
- Andrew Treloar
- Australian National Data Service, Melbourne, Australia
- Sonika Tyagi
- Australian Genome Research Facility Ltd., Melbourne, Australia
- Maarten van Gompel
- Centre for Language and Speech Technology, Radboud University Nijmegen, Nijmegen, Netherlands
- Daniel Vaughan
- EMBL-EBI, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
- Allegra Via
- IBPM-CNR, Department of Biochemical Sciences , Sapienza University of Rome, Rome, Italy
- Xiaochuan Wang
- Faculty of Information Technology, Monash University, Victoria, Australia
- Nathan S. Watson-Haigh
- School of Agriculture, Food & Wine, University of Adelaide, Adelaide, Australia
- Steve Crouch
- Software Sustainability Institute, Web and Internet Science, University of Southampton, Southampton, UK
- DOI
- https://doi.org/10.12688/f1000research.11407.1
- Journal volume & issue
-
Vol. 6
Abstract
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.
Keywords
