And using international digital health groups to engage their members and other relevant stakeholder organisations to use the checklist. After publication, the CODE-EHR framework will undergo a 2-year evaluation, including discussions with researchers using the approach, with a plan for iterative improvements to adapt to the rapidly developing field of medical research. Technological progress has led to rapid progress in heath data systems, with immediate effects in daily clinical practice. The potential for improving patient care and outcomes is clear, as are the challenges and limitations. As with data security, a framework of accountability would enable editorial teams in medical journals to be aware of the technical processes before data analysis.

Unfortunately, code reviews and especially judgments during code reviews can be clouded by bias. For example, a recent study at Google showed that developers that identify as women get more pushback during code reviews than peers that identify as men. Also, other studies look at how race, gender, ethnicity, and age influence the code review experience. And also, these studies find that pushback, code review rejections, and also the scrutiny with which reviews are performed are biased based on those factors. For example, a large-scale study on code review participation and acceptance rate in open source showed that code written by developers that appear to be black is more likely to be rejected than code written by developers who appear to be white. As such, make sure you are aware of the existing bias during code review and proactively take actions to reduce bias, harassment, and prejudice in code reviews.

Whitespace is any space in your code that is not taken up by physical characters. Tabbing is one way to create whitespace in consistent units using the ‘tab’ key. While some languages ignore whitespace and tabbing all together, others entirely rely on the concept. Because of this, it is important to ensure your code is consistently organized. Whitespace and tabbing are often used to clarify nested loops and logical statements.

Code Reviewing in the Trenches: Understanding Challenges, Best Practices and Tool Needs

Use style checkers, syntax checkers and other automated tools like static analysis tools to help improve the code. This way, you make sure that code reviewers can really concentrate on giving valuable feedback and do not need to use their time to comment on issues that can be found automatically. You should select the right number of reviewers for your code change. If more than 4 people come to your mind who should review the code, I’d like you to stop right there. Because adding too many developers to code reviews does more harm than good. 20 Another possibility is for researchers to provide consented and anonymised gold standard cases to benchmark against, or for data from devices used to verify codes .

Reasons linked to discovery were also given by five respondents (3%), for example finding new GitHub repositories of interest and looking for novel code. The REporting of studies Conducted using Observational Routinely-collected health Data statement. Government agencies, regulators, charities, and professional bodies have initiated programmes for better use of real-world data that can support further activity and dissemination.

• Even though less traceable conversations, such as face-to-face or video calls, can make a big difference in team dynamics, it is important to document the discussion.
• The centres at the Barcelona Biomedical Research Park have adopted this set of recommendations and committments governing scientific activities.
• This ensures that they stay in the loop and are aware of what is happening, but removes the obligation for them to comment on your code.
• Whitespace and tabbing are often used to clarify nested loops and logical statements.
• In typical software engineering you have a fairly good idea of the final functionality before writing a single line of code.

You need to actively encourage developers to record every detail so as to avoid past mistakes and gather all the necessary information for future reference. Measuring code quality should be the primary objective of the review process instead of teaching your team to work on different sections. The code should be measured and reviewed in the early stages and in small groups so that all the parts are taken care of. You can use popular code review tools like Git, GitHub, GitLab, and Bitbucket for the same.

Specify any processes used to validate the coding scheme or reference to prior work. Comment on how the observed and any missing data were identified and addressed, and the proportion observed for each variable. The directorate of each PRBB Centre pursuing better code practices will distribute a copy of the new PRBB Code of Good Scientific Practice to all personnel and will provide a copy to any new members when they join the Centre. In both cases, individuals will be required to confirm receipt of their copy.

The problem is that I either spend too long making getting my “research” code to industry-quality, or I publish work based on “bad quality” code, and I feel like a fraud. I sometimes feel as though my industrial experience has been a hindrance in my research, as the goals of writing software in a research context feel contradictory to the goals in industry. I have been a professional software developer for a number of years, I’m also an academic researcher – and my research has involved lots of software development.

This includes the methods used to assess the quality of linkage and the results of any data pre-processing and linkage . Conflicts of interest may be financial or personal and where possible should be avoided. If it is impossible to avoid them, conflicts of interest should be declared by all authors of an article. Any person linked to a research group who requests inclusion as an author on the basis of hierarchical position or professional relationship violates the principles of academic freedom and commits an act of injustice, if not abuse of authority. Likewise, the omission of names of any individuals who have made proven contributions according to the criteria in Section 6.2 represents an act of misappropriation of intellectual property on the part of the other authors.

The same principle is applicable to references to ‘personal communication’. This study explores knowledge sharing in the context of Modern Code Review where engineers assess source code composed by other developers to improve the product quality through knowledge exchange among developers . There is evidence from our survey and others (e.g., Perkel, 2017; Samota & Davey, 2021) that researchers regard the ability to interact with code https://globalcloudteam.com/ published in its complete software environment as beneficial. Platforms that utilise this technology have been adopted or trialled by several publishers, for example Code Ocean has been deployed by some Springer Nature journals, and some Taylor & Francis journals. This survey did not map participants’ workflows so they could be downloading and running code locally, although this is not always easy or possible (Samota & Davey, 2021).

Notify people that benefit from this review

Aiming for 100% perfection that will require double the time is not worth it. “If I heard such a thing, I would not believe anything this person published ever again” – hence, no one publishes really publishes code. Connect and share knowledge within a single location that is structured and easy to search. You can also take a look at a presentation I gave covering the same materials here. I discuss some of the practices in this book with Brian Okken on the Test & Code podcast. Please contact me if you’d like to see a print edition of this book.

In addition, our software development and quality assurance processes must also adhere to international standards and medical devices regulations, in order to receive the necessary certifications that allow the software to be used in a clinical setting. The benefits of code reviews rise and fall with the value of the code review feedback. If done correctly, code reviews can help to ensure a high-quality code base. However, if teams are not aware of and do not follow code review best practices, developers may experience several code review pitfalls.

Code Review: Best Practices

Needless to say my respect for this individual dropped a notch or two, which was unfortunate for him as he hadn’t earned that much in the first place. If nothing else, remember that you may have to revisit your own code some time later. Refactoring usually only happens when both a new person starts working with some old code and they feel they need changes or extensions. On the other hand, in more theoretical CS conferences code is mainly a tool — More accurately, in more theoretical CS conferences, code doesn’t exist at all.

A piece of code that does a single task that can be called whenever required. Check if you’ve to repeat code for different tasks, again and again, so there you can use these functions to reduce the repeatability of code. In this blog, we will discuss the 5 steps to a complete review code.

Samota & Davey state that top-down requirements from journals to release reproducible data and code will in part rely on the availability of technical solutions that are accessible and useful to most scientists. In one sense, these solutions are already available in the form of code repositories, although we acknowledge this doesn’t enforce reproducible code and data sharing because the code is not curated or reviewed. However, technology is only one barrier and the journals that have implemented enhanced solutions are, to our knowledge, yet to show that these are making a significant difference to the quality or amount of code that is shared. Additionally, the added benefit, as opposed to the perceived benefit, that they bring to authors and readers versus the use of other methods of sharing, has not been demonstrated. Is an important way to ensure appropriate data stewardship and privacy, leading to clinical effects through robust publications, regulatory decision making, and practice guidelines. In this Review, we reported a global multistakeholder process to develop a framework for researchers to use in the design and reporting of studies that include structured or coded health-care data.

Code review rises and falls with the quality of the team’s feedback culture. If some feedback made you uncomfortable try to sort things out as soon as possible. Sometimes it is a good idea to have more personal face-to-face conversations to resolve some issues.

All About Coding Quality

There are many different services available for this purpose, most of which rely on the open-source tool Git. Since we are particularly patriotic at Pacmed, we use Gitlab, born and bred in the Netherlands. Nyone who has ever coded even a simple script has likely experienced the pure excitement of seeing their program run for the first time without errors. For Data Scientists in particular, the satisfaction of successfully building and training a machine learning model is probably unrivalled.

In this context, code is written to run the experiment, and might never be looked at again (we are judged on our papers – not our code). There seems to be no motivation to write tested, maintainable, documented code – I just need to run it and get the result in my paper or whatever ASAP. Consequently, the “academic” code I’ve written is poor quality – from a software engineering perspective. For every rule that you’re stating in the code, there should be clear reasoning as to why the code is expected to follow a certain rule. This should also include compliant and non-compliant examples and exceptions to observe a smooth software development environment.

Comparing policy to technology as solutions for increasing code sharing

Interestingly, in our studies, we observed that developers really appreciate code change descriptions. Counterintuitively, we saw that the same developers that wished others would prepare code review descriptions did not always include descriptions themselves. If several changes with different purposes happen within one code review, the task of code reviewing becomes more difficult. Although computers have been used in science for decades, it seems that algorithms have only become an important part of research in the last decade or so (perhaps because of “big data”). When you base your research on code, that code must be good quality.

Give respectful and constructive feedback

Data privacy and the licence for research can be severely compromised if linkage is not secure. Therefore, our focus is on transparency about how data are coded and linked and how these approaches undertaken by researchers are openly discussed and documented. The stakeholder consensus meetings highlighted clarity of methods as an important concern for future research, supported by evidence that few studies provide sufficient detail to understand the research process. 23 is an important way to ensure appropriate data stewardship and privacy, leading to clinical impact through robust publications, regulatory decision making, and practice guidelines.

As such, focusing on the units of the code that need to be properly tested is the way to go. This would not only improve code quality but also identify potential errors beforehand. SOLID principles are nothing but a set of rules and best practices introduced by the famous Computer Scientist Robert J. Martin that you need to follow while approaching Object-Oriented class design. These rules help your programmers understand the need for precise design patterns and software architecture as a whole.

Provide a code review description

It increases the maintainability of the code, decreases manual testing costs, and helps to reduce post-production defects. So, as a best practice for code reviews, when designing your personal code review schedule, check the time zones of your peers. It might make a big difference for someone if you dedicate half an hour in the morning instead of in the afternoon to do code reviews, while for yourself, it might not be that big of a deal.

Konkol M, Nüst D, Goulier L. Publishing computational research—a review of infrastructures for reproducible and transparent scholarly communication. Colavizza G, Hrynaszkiewicz I, Staden I, Whitaker K, McGillivray B. The citation advantage of linking publications to research data. The authors thank James Harney, Gary Beardmore, Helen McDonald and Philip Mills from PLOS for their contributions to the survey work. We also thank James Harney, Marcel LaFlamme and Dan Morgan from PLOS and Professor Jason Papin, University of Virginia and PLOS Computational Biology co-Editor-in-Chief, for comments on an earlier version of this manuscript.