Four simple recommendations to encourage best practices in research software

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

doi:10.12688/f1000research.11407.1

Four simple recommendations to encourage best practices in research software

F1000Res. 2017 Jun 13:6:ELIXIR-876. doi: 10.12688/f1000research.11407.1. eCollection 2017.

Authors

Rafael C Jiménez¹, Mateusz Kuzak², Monther Alhamdoosh³, Michelle Barker⁴, Bérénice Batut⁵, Mikael Borg⁶, Salvador Capella-Gutierrez⁷, Neil Chue Hong⁸, Martin Cook¹, Manuel Corpas⁹, Madison Flannery¹⁰, Leyla Garcia¹¹, Josep Ll Gelpí^{12

13}, Simon Gladman¹⁰, Carole Goble¹⁴, Montserrat González Ferreiro¹¹, Alejandra Gonzalez-Beltran¹⁵, Philippa C Griffin¹⁰, Björn Grüning⁵, Jonas Hagberg⁶, Petr Holub¹⁶, Rob Hooft¹⁷, Jon Ison¹⁸, Daniel S Katz^{19

20

21

22}, Brane Leskošek²³, Federico López Gómez¹, Luis J Oliveira²⁴, David Mellor²⁵, Rowland Mosbergen²⁶, Nicola Mulder²⁷, Yasset Perez-Riverol¹¹, Robert Pergl²⁸, Horst Pichler²⁹, Bernard Pope¹⁰, Ferran Sanz³⁰, Maria V Schneider¹⁰, Victoria Stodden²⁰, Radosław Suchecki³¹, Radka Svobodová Vařeková^{32

33}, Harry-Anton Talvik³⁴, Ilian Todorov³⁵, Andrew Treloar³⁶, Sonika Tyagi^{10

37}, Maarten van Gompel³⁸, Daniel Vaughan¹¹, Allegra Via³⁹, Xiaochuan Wang⁴⁰, Nathan S Watson-Haigh³¹, Steve Crouch⁴¹

Affiliations

¹ ELIXIR Hub, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.
² Netherlands eScience Center, Science Park 140, Amsterdam, 1098 XG, Netherlands.
³ CSL Limited, Bio21 Institute, 30 Flemington Road, Parkville, Victoria, 3010, Australia.
⁴ National eResearch Collaboration Tools and Resources, Victoria, 3010, Australia.
⁵ ELIXIR-DE and de.NBI, Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany.
⁶ ELIXIR-SE, National Bioinformatics Infrastructure Sweden (NBIS), Scilifelab, Department of Biochemistry and Biophysics (DBB), Stockholm University, Stockholm, Sweden.
⁷ ELIXIR-ES, Spanish National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Almagro 3, Madrid, 28029, Spain.
⁸ Software Sustainability Institute, JCMB, University of Edinburgh, Edinburgh, EH9 3FD, UK.
⁹ Repositive Ltd, Future Business Centre, Cambridge, UK.
¹⁰ EMBL Australia Bioinformatics Resource, Lab-14, The University of Melbourne, 700 Swanston St, Parkville, Victoria, 3053, Australia.
¹¹ EMBL-EBI, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.
¹² Barcelona Supercomputing Center, Barcelona, 08034, Spain.
¹³ Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, Barcelona, 08028, Spain.
¹⁴ ELIXIR-UK, Software Sustainability Institute, School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
¹⁵ Oxford e-Research Centre, University of Oxford, Oxford, UK.
¹⁶ BBMRI-ERIC, Neue Stiftingtalstraße 2/B/6, Graz, 8010, Austria.
¹⁷ Dutch TechCenter for Life Sciences and ELIXIR-NL, Utrecht, Netherlands.
¹⁸ ELIXIR-DK, Technical University of Denmark, Denmark, Denmark.
¹⁹ National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
²⁰ School of Information Sciences, University of Illinois Urbana Champaign, Urbana, IL, USA.
²¹ Department of Electrical and Computer Engineering, University of Illinois Urbana Champaign, Urbana, IL, USA.
²² Department of Computer Science, University of Illinois Urbana Champaign, Urbana, IL, USA.
²³ ELIXIR-SI, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
²⁴ DETI/IEETA, University of Aveiro, Aveiro, Portugal.
²⁵ Center for Open Science, Charlottesville, VA, USA.
²⁶ Stemformatics, University of Melbourne, Melbourne, Australia.
²⁷ Computational Biology Division, Department of Integrative Biomedical Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
²⁸ ELIXIR-CZ, Faculty of Information Technology, Czech Technical University in Prague, Prague, Czech Republic.
²⁹ BBMRI.at, Alpen-Adria-University Klagenfurt, Klagenfurt, Austria.
³⁰ GRIB, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Universitat Pompeu Fabra, Barcelona, Spain.
³¹ School of Agriculture, Food & Wine, University of Adelaide, Adelaide, Australia.
³² Central European Institute of Technology (CEITEC), Brno, Czech Republic.
³³ National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic.
³⁴ ELIXIR-EE, Institute of Computer Science, University of Tartu, Tartu, Estonia.
³⁵ Science & Technologies Facilities Council, Swindon, UK.
³⁶ Australian National Data Service, Melbourne, Australia.
³⁷ Australian Genome Research Facility Ltd., Melbourne, Australia.
³⁸ Centre for Language and Speech Technology, Radboud University Nijmegen, Nijmegen, Netherlands.
³⁹ IBPM-CNR, Department of Biochemical Sciences , Sapienza University of Rome, Rome, Italy.
⁴⁰ Faculty of Information Technology, Monash University, Victoria, Australia.
⁴¹ Software Sustainability Institute, Web and Internet Science, University of Southampton, Southampton, UK.

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: FAIR; Open Science; Open Source; best practices; code; guidelines; quality; recommendations; software; sustainability.

Grants and funding

This work was partially supported by ELIXIR-EXCELERATE and CORBEL. ELIXIR-EXCELERATE and CORBEL are funded by the European Commission within the Research Infrastructures programme of Horizon 2020, grant agreement numbers 676559 and 654248. The European workshops were supported by ELIXIR and organised in collaboration with the Software Sustainability Institute and Netherlands eScience Center. The workshop in Australia was supported by EMBL-ABR via its main funders: The University of Melbourne and Bioplatforms Australia.