Four simple recommendations to encourage best practices in research software [version 1; referees: 2 approved]
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 adopt...
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| Format: | Article |
| Language: | English |
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F1000 Research Ltd
2017-06-01
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| Series: | F1000Research |
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| Online Access: | https://f1000research.com/articles/6-876/v1 |
| _version_ | 1819295445774499840 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Rafael C. Jiménez |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-24T04:42:20Z |
| format | Article |
| id | doaj.art-ae593f223a074427850b1fb626642ba4 |
| institution | Directory Open Access Journal |
| issn | 2046-1402 |
| language | English |
| last_indexed | 2024-12-24T04:42:20Z |
| publishDate | 2017-06-01 |
| publisher | F1000 Research Ltd |
| record_format | Article |
| series | F1000Research |
| spelling | doaj.art-ae593f223a074427850b1fb626642ba42022-12-21T17:14:47ZengF1000 Research LtdF1000Research2046-14022017-06-01610.12688/f1000research.11407.112314Four simple recommendations to encourage best practices in research software [version 1; referees: 2 approved]Rafael C. Jiménez0Mateusz Kuzak1Monther Alhamdoosh2Michelle Barker3Bérénice Batut4Mikael Borg5Salvador Capella-Gutierrez6Neil Chue Hong7Martin Cook8Manuel Corpas9Madison Flannery10Leyla Garcia11Josep Ll. Gelpí12Simon Gladman13Carole Goble14Montserrat González Ferreiro15Alejandra Gonzalez-Beltran16Philippa C. Griffin17Björn Grüning18Jonas Hagberg19Petr Holub20Rob Hooft21Jon Ison22Daniel S. Katz23Brane Leskošek24Federico López Gómez25Luis J. Oliveira26David Mellor27Rowland Mosbergen28Nicola Mulder29Yasset Perez-Riverol30Robert Pergl31Horst Pichler32Bernard Pope33Ferran Sanz34Maria V. Schneider35Victoria Stodden36Radosław Suchecki37Radka Svobodová Vařeková38Harry-Anton Talvik39Ilian Todorov40Andrew Treloar41Sonika Tyagi42Maarten van Gompel43Daniel Vaughan44Allegra Via45Xiaochuan Wang46Nathan S. Watson-Haigh47Steve Crouch48ELIXIR Hub, Wellcome Genome Campus, Hinxton, CB10 1SD, UKNetherlands eScience Center, Science Park 140, Amsterdam, 1098 XG, NetherlandsCSL Limited, Bio21 Institute, 30 Flemington Road, Parkville, Victoria, 3010, AustraliaNational eResearch Collaboration Tools and Resources, Victoria, 3010, AustraliaELIXIR-DE and de.NBI, Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, GermanyELIXIR-SE, National Bioinformatics Infrastructure Sweden (NBIS), Scilifelab, Department of Biochemistry and Biophysics (DBB), Stockholm University, Stockholm, SwedenELIXIR-ES, Spanish National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Almagro 3, Madrid, 28029, SpainSoftware Sustainability Institute, JCMB, University of Edinburgh, Edinburgh, EH9 3FD, UKELIXIR Hub, Wellcome Genome Campus, Hinxton, CB10 1SD, UKRepositive Ltd, Future Business Centre, Cambridge, UKEMBL Australia Bioinformatics Resource, Lab-14, The University of Melbourne, 700 Swanston St, Parkville, Victoria, 3053, AustraliaEMBL-EBI, Wellcome Genome Campus, Hinxton, CB10 1SD, UKDepartment of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, Barcelona, 08028, SpainEMBL Australia Bioinformatics Resource, Lab-14, The University of Melbourne, 700 Swanston St, Parkville, Victoria, 3053, AustraliaELIXIR-UK, Software Sustainability Institute, School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UKEMBL-EBI, Wellcome Genome Campus, Hinxton, CB10 1SD, UKOxford e-Research Centre, University of Oxford, Oxford, UKEMBL Australia Bioinformatics Resource, Lab-14, The University of Melbourne, 700 Swanston St, Parkville, Victoria, 3053, AustraliaELIXIR-DE and de.NBI, Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, GermanyELIXIR-SE, National Bioinformatics Infrastructure Sweden (NBIS), Scilifelab, Department of Biochemistry and Biophysics (DBB), Stockholm University, Stockholm, SwedenBBMRI-ERIC, Neue Stiftingtalstraße 2/B/6, Graz, 8010, AustriaDutch TechCenter for Life Sciences and ELIXIR-NL, Utrecht, NetherlandsELIXIR-DK, Technical University of Denmark, Denmark, DenmarkDepartment of Computer Science, University of Illinois Urbana Champaign, Urbana, IL, USAELIXIR-SI, Faculty of Medicine, University of Ljubljana, Ljubljana, SloveniaELIXIR Hub, Wellcome Genome Campus, Hinxton, CB10 1SD, UKDETI/IEETA, University of Aveiro, Aveiro, PortugalCenter for Open Science, Charlottesville, VA, USAStemformatics, University of Melbourne, Melbourne, AustraliaComputational Biology Division, Department of Integrative Biomedical Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South AfricaEMBL-EBI, Wellcome Genome Campus, Hinxton, CB10 1SD, UKELIXIR-CZ, Faculty of Information Technology, Czech Technical University in Prague, Prague, Czech RepublicBBMRI.at, Alpen-Adria-University Klagenfurt, Klagenfurt, AustriaEMBL Australia Bioinformatics Resource, Lab-14, The University of Melbourne, 700 Swanston St, Parkville, Victoria, 3053, AustraliaGRIB, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), Universitat Pompeu Fabra, Barcelona, SpainEMBL Australia Bioinformatics Resource, Lab-14, The University of Melbourne, 700 Swanston St, Parkville, Victoria, 3053, AustraliaSchool of Information Sciences, University of Illinois Urbana Champaign, Urbana, IL, USASchool of Agriculture, Food & Wine, University of Adelaide, Adelaide, AustraliaNational Centre for Biomolecular Research, Masaryk University, Brno, Czech RepublicELIXIR-EE, Institute of Computer Science, University of Tartu, Tartu, EstoniaScience & Technologies Facilities Council, Swindon, UKAustralian National Data Service, Melbourne, AustraliaAustralian Genome Research Facility Ltd., Melbourne, AustraliaCentre for Language and Speech Technology, Radboud University Nijmegen, Nijmegen, NetherlandsEMBL-EBI, Wellcome Genome Campus, Hinxton, CB10 1SD, UKIBPM-CNR, Department of Biochemical Sciences , Sapienza University of Rome, Rome, ItalyFaculty of Information Technology, Monash University, Victoria, AustraliaSchool of Agriculture, Food & Wine, University of Adelaide, Adelaide, AustraliaSoftware Sustainability Institute, Web and Internet Science, University of Southampton, Southampton, UKScientific 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.https://f1000research.com/articles/6-876/v1BioinformaticsData Sharing |
| spellingShingle | 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 Four simple recommendations to encourage best practices in research software [version 1; referees: 2 approved] F1000Research Bioinformatics Data Sharing |
| title | Four simple recommendations to encourage best practices in research software [version 1; referees: 2 approved] |
| title_full | Four simple recommendations to encourage best practices in research software [version 1; referees: 2 approved] |
| title_fullStr | Four simple recommendations to encourage best practices in research software [version 1; referees: 2 approved] |
| title_full_unstemmed | Four simple recommendations to encourage best practices in research software [version 1; referees: 2 approved] |
| title_short | Four simple recommendations to encourage best practices in research software [version 1; referees: 2 approved] |
| title_sort | four simple recommendations to encourage best practices in research software version 1 referees 2 approved |
| topic | Bioinformatics Data Sharing |
| url | https://f1000research.com/articles/6-876/v1 |
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