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Improving Science That Uses Code

Harold Thimbleby Orcid Logo

The Computer Journal

Swansea University Author: Harold Thimbleby Orcid Logo

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DOI (Published version): 10.1093/comjnl/bxad067

Abstract

As code is now an inextricable part of science it should be supported by competent Software Engineering, analogously to statistical claims being properly supported by competent statistics.If and when code avoids adequate scrutiny, science becomes unreliable and unverifiable because results — text, d...

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Published in: The Computer Journal
ISSN: 0010-4620 1460-2067
Published: Oxford University Press (OUP) 2023
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URI: https://cronfa.swan.ac.uk/Record/cronfa63873
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Even when available, scientists rarely provide adequate documentation to understand or use it reliably.This paper proposes and justifies ways to improve science using code:1. Professional Software Engineers can help, particularly in critical fields such as public health, climate change and energy.2. ‘Software Engineering Boards,’ analogous to Ethics or Institutional Review Boards, should be instigated and used.3. The Reproducible Analytic Pipeline (RAP) methodology can be generalized to cover code and Software Engineering methodologies, in a generalization this paper introduces called RAP+. RAP+ (or comparable interventions) could be supported and or even required in journal, conference and funding body policies.The paper’s Supplemental Material provides a summary of Software Engineering best practice relevant to scientific research, including further suggestions for RAP+ workflows.‘Science is what we understand well enough to explain to a computer.’ Donald E. Knuth in A=B [ 1]‘I have to write to discover what I am doing.’ Flannery O’Connor, quoted in Write for your life [ 2]‘Criticism is the mother of methodology.’ Robert P. 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Published by Oxford University Press on behalf of The British Computer Society. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.</documentNotes><copyrightCorrect>true</copyrightCorrect><language>eng</language><licence>https://creativecommons.org/licenses/by/4.0/</licence></document></documents><OutputDurs/></rfc1807>
spelling v2 63873 2023-07-12 Improving Science That Uses Code c12beb0ab0e333a9a512589d411d17f3 0000-0003-2222-4243 Harold Thimbleby Harold Thimbleby true false 2023-07-12 FGSEN As code is now an inextricable part of science it should be supported by competent Software Engineering, analogously to statistical claims being properly supported by competent statistics.If and when code avoids adequate scrutiny, science becomes unreliable and unverifiable because results — text, data, graphs, images, etc — depend on untrustworthy code.Currently, scientists rarely assure the quality of the code they rely on, and rarely make it accessible for scrutiny. Even when available, scientists rarely provide adequate documentation to understand or use it reliably.This paper proposes and justifies ways to improve science using code:1. Professional Software Engineers can help, particularly in critical fields such as public health, climate change and energy.2. ‘Software Engineering Boards,’ analogous to Ethics or Institutional Review Boards, should be instigated and used.3. The Reproducible Analytic Pipeline (RAP) methodology can be generalized to cover code and Software Engineering methodologies, in a generalization this paper introduces called RAP+. RAP+ (or comparable interventions) could be supported and or even required in journal, conference and funding body policies.The paper’s Supplemental Material provides a summary of Software Engineering best practice relevant to scientific research, including further suggestions for RAP+ workflows.‘Science is what we understand well enough to explain to a computer.’ Donald E. Knuth in A=B [ 1]‘I have to write to discover what I am doing.’ Flannery O’Connor, quoted in Write for your life [ 2]‘Criticism is the mother of methodology.’ Robert P. Abelson in Statistics as Principled Argument [ 3]‘From its earliest times, science has operated by being open and transparent about methods and evidence, regardless of which technology has been in vogue.’ Editorial in Nature [4] Journal Article The Computer Journal Oxford University Press (OUP) 0010-4620 1460-2067 Computational Science, Software Engineering, reproducibility, scientific scrutiny, reproducible analytic pipeline (RAP &amp; RAP+) 23 8 2023 2023-08-23 10.1093/comjnl/bxad067 http://dx.doi.org/10.1093/comjnl/bxad067 COLLEGE NANME Science and Engineering - Faculty COLLEGE CODE FGSEN Swansea University SU Library paid the OA fee (TA Institutional Deal) This work was jointly supported by See Change (M&RA-P), Scotland (an anonymous funder), by the Engineering and Physical Sciences Research Council [grant EP/M022722/1], by the Royal Academy of Engineering through the Engineering X Pandemic Preparedness Programme [grant EXPP2021\1\186] and by Assuring Autonomy International Programme, Assuring Safe AI in Ambulance Service Triage. The funders had no involvement in the research or in this paper. grant EP/M022722/1 2023-12-08T16:02:54.4443528 2023-07-12T12:41:37.2553680 Faculty of Medicine, Health and Life Sciences Swansea University Medical School - Health Data Science Harold Thimbleby 0000-0003-2222-4243 1 63873__28460__76b6bd580add4f66b252eb6f79484abc.pdf 63873 vor.pdf 2023-09-05T16:02:27.1861829 Output 880442 application/pdf Version of Record true © The Author(s) 2023. Published by Oxford University Press on behalf of The British Computer Society. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. true eng https://creativecommons.org/licenses/by/4.0/
title Improving Science That Uses Code
spellingShingle Improving Science That Uses Code
Harold Thimbleby
title_short Improving Science That Uses Code
title_full Improving Science That Uses Code
title_fullStr Improving Science That Uses Code
title_full_unstemmed Improving Science That Uses Code
title_sort Improving Science That Uses Code
author_id_str_mv c12beb0ab0e333a9a512589d411d17f3
author_id_fullname_str_mv c12beb0ab0e333a9a512589d411d17f3_***_Harold Thimbleby
author Harold Thimbleby
author2 Harold Thimbleby
format Journal article
container_title The Computer Journal
publishDate 2023
institution Swansea University
issn 0010-4620
1460-2067
doi_str_mv 10.1093/comjnl/bxad067
publisher Oxford University Press (OUP)
college_str Faculty of Medicine, Health and Life Sciences
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hierarchy_top_title Faculty of Medicine, Health and Life Sciences
hierarchy_parent_id facultyofmedicinehealthandlifesciences
hierarchy_parent_title Faculty of Medicine, Health and Life Sciences
department_str Swansea University Medical School - Health Data Science{{{_:::_}}}Faculty of Medicine, Health and Life Sciences{{{_:::_}}}Swansea University Medical School - Health Data Science
url http://dx.doi.org/10.1093/comjnl/bxad067
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description As code is now an inextricable part of science it should be supported by competent Software Engineering, analogously to statistical claims being properly supported by competent statistics.If and when code avoids adequate scrutiny, science becomes unreliable and unverifiable because results — text, data, graphs, images, etc — depend on untrustworthy code.Currently, scientists rarely assure the quality of the code they rely on, and rarely make it accessible for scrutiny. Even when available, scientists rarely provide adequate documentation to understand or use it reliably.This paper proposes and justifies ways to improve science using code:1. Professional Software Engineers can help, particularly in critical fields such as public health, climate change and energy.2. ‘Software Engineering Boards,’ analogous to Ethics or Institutional Review Boards, should be instigated and used.3. The Reproducible Analytic Pipeline (RAP) methodology can be generalized to cover code and Software Engineering methodologies, in a generalization this paper introduces called RAP+. RAP+ (or comparable interventions) could be supported and or even required in journal, conference and funding body policies.The paper’s Supplemental Material provides a summary of Software Engineering best practice relevant to scientific research, including further suggestions for RAP+ workflows.‘Science is what we understand well enough to explain to a computer.’ Donald E. Knuth in A=B [ 1]‘I have to write to discover what I am doing.’ Flannery O’Connor, quoted in Write for your life [ 2]‘Criticism is the mother of methodology.’ Robert P. Abelson in Statistics as Principled Argument [ 3]‘From its earliest times, science has operated by being open and transparent about methods and evidence, regardless of which technology has been in vogue.’ Editorial in Nature [4]
published_date 2023-08-23T16:02:54Z
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