Four simple recommendations to encourage best practices in research software  [version 1; referees: 3 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

doi:10.12688/f1000research.11407.1

Four simple recommendations to encourage best practices in research software [version 1; referees: 3 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 HagbergPetr 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

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Article number	876
Number of pages	13
Journal	F1000Research
Volume	6
DOIs	https://doi.org/10.12688/f1000research.11407.1
Publication status	Published - 13 Jun 2017

Keywords / Materials (for Non-textual outputs)

Best practices
Code
FAIR
Guidelines
Open Science
Open Source
Quality
Recommendations
Software
Sustainability

Access to Document

10.12688/f1000research.11407.1

62943d2e-4156-4ef3-a878-55990b84da2e_11407_-_rafael_c_jimenezFinal published version, 1.02 MBLicence: Creative Commons: Attribution (CC-BY)

Cite this

Jiménez, R. C., Kuzak, M., Alhamdoosh, M., Barker, M., Batut, B., Borg, M., Capella-Gutierrez, S., Chue Hong, N., Cook, M., Corpas, M., Flannery, M., Garcia, L., Gelpí, J. L., Gladman, S., Goble, C., González Ferreiro, M., Gonzalez-Beltran, A., Griffin, P. C., Grüning, B., ... Crouch, S. (2017). Four simple recommendations to encourage best practices in research software [version 1; referees: 3 approved]. F1000Research, 6, Article 876. https://doi.org/10.12688/f1000research.11407.1

@article{c55b1d912ad54f6a8df7bc319994aa2e,

title = "Four simple recommendations to encourage best practices in research software [version 1; referees: 3 approved]",

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 = "Best practices, Code, FAIR, Guidelines, Open Science, Open Source, Quality, Recommendations, Software, Sustainability",

author = "Jim{\'e}nez, {Rafael C.} and Mateusz Kuzak and Monther Alhamdoosh and Michelle Barker and B{\'e}r{\'e}nice Batut and Mikael Borg and Salvador Capella-Gutierrez and {Chue Hong}, Neil and Martin Cook and Manuel Corpas and Madison Flannery and Leyla Garcia and Gelp{\'i}, {Josep Ll} and Simon Gladman and Carole Goble and {Gonz{\'a}lez Ferreiro}, Montserrat and Alejandra Gonzalez-Beltran and Griffin, {Philippa C.} and Bj{\"o}rn Gr{\"u}ning and Jonas Hagberg and Petr Holub and Rob Hooft and Jon Ison and Katz, {Daniel S.} and Brane Lesko{\v s}ek and {L{\'o}pez G{\'o}mez}, Federico and Oliveira, {Luis J.} and David Mellor and Rowland Mosbergen and Nicola Mulder and Yasset Perez-Riverol and Robert Pergl and Horst Pichler and Bernard Pope and Ferran Sanz and Schneider, {Maria V.} and Victoria Stodden and Rados{\l}aw Suchecki and {Svobodov{\'a} Va{\v r}ekov{\'a}}, Radka and Talvik, {Harry Anton} and Ilian Todorov and Andrew Treloar and Sonika Tyagi and {van Gompel}, Maarten and Daniel Vaughan and Allegra Via and Xiaochuan Wang and Watson-Haigh, {Nathan S.} and Steve Crouch",

year = "2017",

month = jun,

day = "13",

doi = "10.12688/f1000research.11407.1",

language = "English",

volume = "6",

journal = "F1000Research",

issn = "2046-1402",

publisher = "Taylor & Francis",

}

Jiménez, RC, Kuzak, M, Alhamdoosh, M, Barker, M, Batut, B, Borg, M, Capella-Gutierrez, S, Chue Hong, N, Cook, M, Corpas, M, Flannery, M, Garcia, L, Gelpí, JL, Gladman, S, Goble, C, González Ferreiro, M, Gonzalez-Beltran, A, Griffin, PC, Grüning, B, Hagberg, J, Holub, P, Hooft, R, Ison, J, Katz, DS, Leskošek, B, López Gómez, F, Oliveira, LJ, Mellor, D, Mosbergen, R, Mulder, N, Perez-Riverol, Y, Pergl, R, Pichler, H, Pope, B, Sanz, F, Schneider, MV, Stodden, V, Suchecki, R, Svobodová Vařeková, R, Talvik, HA, Todorov, I, Treloar, A, Tyagi, S, van Gompel, M, Vaughan, D, Via, A, Wang, X, Watson-Haigh, NS & Crouch, S 2017, 'Four simple recommendations to encourage best practices in research software [version 1; referees: 3 approved]', F1000Research, vol. 6, 876. https://doi.org/10.12688/f1000research.11407.1

TY - JOUR

T1 - Four simple recommendations to encourage best practices in research software [version 1; referees: 3 approved]

AU - Jiménez, Rafael C.

AU - Kuzak, Mateusz

AU - Alhamdoosh, Monther

AU - Barker, Michelle

AU - Batut, Bérénice

AU - Borg, Mikael

AU - Capella-Gutierrez, Salvador

AU - Chue Hong, Neil

AU - Cook, Martin

AU - Corpas, Manuel

AU - Flannery, Madison

AU - Garcia, Leyla

AU - Gelpí, Josep Ll

AU - Gladman, Simon

AU - Goble, Carole

AU - González Ferreiro, Montserrat

AU - Gonzalez-Beltran, Alejandra

AU - Griffin, Philippa C.

AU - Grüning, Björn

AU - Hagberg, Jonas

AU - Holub, Petr

AU - Hooft, Rob

AU - Ison, Jon

AU - Katz, Daniel S.

AU - Leskošek, Brane

AU - López Gómez, Federico

AU - Oliveira, Luis J.

AU - Mellor, David

AU - Mosbergen, Rowland

AU - Mulder, Nicola

AU - Perez-Riverol, Yasset

AU - Pergl, Robert

AU - Pichler, Horst

AU - Pope, Bernard

AU - Sanz, Ferran

AU - Schneider, Maria V.

AU - Stodden, Victoria

AU - Suchecki, Radosław

AU - Svobodová Vařeková, Radka

AU - Talvik, Harry Anton

AU - Todorov, Ilian

AU - Treloar, Andrew

AU - Tyagi, Sonika

AU - van Gompel, Maarten

AU - Vaughan, Daniel

AU - Via, Allegra

AU - Wang, Xiaochuan

AU - Watson-Haigh, Nathan S.

AU - Crouch, Steve

PY - 2017/6/13

Y1 - 2017/6/13

N2 - 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.

AB - 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.

KW - Best practices

KW - Code

KW - FAIR

KW - Guidelines

KW - Open Science

KW - Open Source

KW - Quality

KW - Recommendations

KW - Software

KW - Sustainability

UR - http://www.scopus.com/inward/record.url?scp=85024481292&partnerID=8YFLogxK

U2 - 10.12688/f1000research.11407.1

DO - 10.12688/f1000research.11407.1

M3 - Article

AN - SCOPUS:85024481292

SN - 2046-1402

VL - 6

JO - F1000Research

JF - F1000Research

M1 - 876

ER -

Four simple recommendations to encourage best practices in research software [version 1; referees: 3 approved]

Abstract

Keywords / Materials (for Non-textual outputs)

Access to Document

Other files and links

Fingerprint

The Software Sustainability Institute: Phase 2

Introducing the FAIR Principles for research software

Towards FAIR principles for research software

Top 10 metrics for life science software good practices [version 1; referees: 2 approved]

Neil Chue Hong

Cite this

Four simple recommendations to encourage best practices in research software [version 1; referees: 3 approved]

Abstract

Keywords / Materials (for Non-textual outputs)

Access to Document

Other files and links

Fingerprint

Projects

The Software Sustainability Institute: Phase 2

Research output

Introducing the FAIR Principles for research software

Towards FAIR principles for research software

Top 10 metrics for life science software good practices [version 1; referees: 2 approved]

Profiles

Neil Chue Hong

Cite this