Code review for application notes

Note: this post is a guest post by Jerome Kelleher. Please also see his letter to Bioinformatics on this topic.


  1. Many journals provide a mechanism to publish computer programs in the form of application notes or software articles. These notes are subject to peer review, but there is no explicit requirement that the quality of the application be taken into account.
  2. Even if reviewers examine the source code, there is no reason to expect that they can provide an informed opinion on its quality. Reviewers are experts in the application domain but not necessarily in the programming language(s) in question.
  3. A system of lightweight code review would greatly improve the quality of the applications available to the community, and incentivize well-written code. Along with the existing scientific review, source code for an application should be reviewed by an expert programmer who would provide an opinion on the overall quality of the application, as well as feedback to the developers on how it may be improved. The code reviewer would not be expected to understand the application in any deep sense, and would provide feedback only on the obvious signals of quality, such as structure, style, consistency, installation instructions, portability, user interface design and so on.
  4. Since code reviewers do not need to understand the application domain they can be drawn from the wider developer community. Ideally, contributors to free and open source projects should be recruited, since these are people with verifiable expertise and a history of contributing their time to a common good. Reviews should not be too time-consuming (a maximum of one hour, say), and there should be public acknowledgement of a reviewer's contribution to a journal.
  5. The benefits would be an immediate improvement in the quality of published applications. The majority of problems in scientific applications not caused by fundamental errors in the methods, but by superficial issues that arise through inexperience. Introducing this limited form of code review would also yield valuable insights for the larger goal of making all scientific code subject to peer review.

The problem

A couple of years ago, I reviewed an application note for Bioinformatics. As part of the review process, I downloaded the Python source code and examined it to get a feel for the quality of the application. It was so poorly written that I immediately formed the judgment that this application could not be trusted, and should be immediately rejected. The source code showed clear evidence of being written by an unsupervised novice programmer. For example, one function took 25 parameters and was 1130 lines long. Within this function, there were 107 conditional statements, indented by up to 9 levels. The same 18 lines of code were repeated (complete with identical comments) thirty six times, with only integer constants changing between each repeated block. Basic mistakes such as these had been made throughout the code base.

The application note was rejected, as the other reviewers also had serious issues with the work. Neither of them, however, brought up the issue of the quality of the code, which in my opinion was sufficient grounds for rejection, regardless of whether the application appeared to work or not. The peer review system worked in this instance, but it had failed before. This particular application had been published by another journal (the authors had been seeking a "version 2.0" publication at Bioinformatics), and had been used and cited in several papers.

Application notes perform an important role, as they provide a forum for researchers to publicize useful code. Most importantly, they provide a mechanism by which researchers can be given due credit for the work involved in developing these important tools. Without the reward mechanism of application note publications and citations, there is simply no incentive to develop tools that are useful to the wider community.

These tools, however, are often of lamentably low quality. Installation can be difficult, and documentation sparse and poor. User interfaces (command line or graphical) rarely follow established conventions, making each tool a challenge to use. The quality of source code is often rather poor, making any reuse or modification very difficult.

The problem is that there is no requirement that the reviewers of an application note examine the source code. Most reviewers will download the application and ensure that it installs and runs on example data. The main goal of a review is to assess the novelty and importance of the methods, not the quality of the software. Because there is no assessment of quality there is no incentive for quality. I believe that this is a major flaw in the review process for scientific software, and so I wrote a letter of the editors of Bioinformatics in which I suggested the introduction of a system of code review for application notes. The editors declined to publish this letter.

Lightweight code review

My suggestion is to introduce a system of lightweight code review for application notes. For many open source projects, code review is an intrinsic part of the development process. A developer submits a patch implementing some new feature for review. Other developers then assess this patch, to ensure that it meets the required standards, and only after it has been reviewed will the code be committed. There are other forms of code review, but these usually involve one developer trying to fully understand the code another has written in order to improve code quality.

This type of code review would not be feasible in the context of application notes. It would be far too laborious, because it would require a reviewer to fully understand all aspects of an application they have never seen before. Instead, I suggest a much more lightweight review process. Code should be assessed for the more obvious signals of quality: readability, consistency, documentation, structure and packaging. Code should follow the idioms of the language involved and should consistently follow a well-known coding style. It should be well documented and appropriately commented. The structure of the code should be clear, and it should be straightforward to find where a particular piece of functionality is implemented.

There is a problem, of course, in finding people to perform these reviews. It would seem that we need reviewers who are both experts in the application domain and in the programming language(s) in question, and such people might be very difficult to find. The solution to this problem is to split the responsibility: experts in the application domain review the manuscript and application for novelty and utility to the community, and expert programmers review the source code in terms of its apparent quality. We are then free to choose code reviewers from anywhere, even from outside of science. An expert programmer could perform a lightweight review in less than an hour and so the demands on their time should not be be too great.

Careful guidelines would be required for reviewers to ensure that reviews remain helpful. For example, it should be made quite clear that disagreements on aesthetic grounds are not appropriate. Once code is consistent, idiomatic and follows some well-known style, it does not matter which particular style it follows.

Reviewers must be experts in the language that the application is written in, and must have a proven track record of delivering high-quality software. Convincing such people to donate their time to review scientific code is the most difficult part of this process, but there are encouraging signs that it may be possible. In a recent pilot study, Mozilla engineers reviewed snippets of source code from previously published PLOS Computational Biology papers. This study found that the engineers were happy to perform the reviews, but were frustrated by the shallowness of the reviews as a result of their lack of domain expertise. All of the reviewers indicated that they were willing to continue to participate in scientific code review "provided they felt they could contribute something of value."

Such shallow (or lightweight) reviews are precisely what is required for application notes. By writing reviews, pointing out the weaknesses of applications and indicating how to fix them, reviewers can enter into a dialogue with application authors. Their expertise would be highly valued, and provide a great service to the academic community, helping to improve the quality of the software used to progress science.

The benefits

It may seem that there is little point in such a lightweight code review process. If a reviewer is only going to spend an hour browsing the code and writing a report, then they will surely miss all sorts of bugs. This is true, and bugs will remain in applications regardless of how much review is done. The point is not to make the software published in application notes perfect, as this is impossible. The point is to try to ensure that published software is reasonably good, as this would be a major improvement.

There would be many benefits. The first would be an increase in the quality of the applications published. Through the influence of the expert reviewers, software would be easier to install and use. Feedback through reviews may also result in improved performance, since reviewers may point out ways in which implementation could be improved. Ultimately, reviewers may choose to contribute code directly to a project, if they see that their help would make a difference and be appreciated. This influx of experience and knowledge would be a huge boon for science.

Another benefit would be an increased realization that significant applications cannot be written by untrained novice programmers. Applications submitted that are of very low quality (such as the example discussed above) should be immediately rejected. A few manuscript rejections may be required before the message filters through, but the message will surely be received eventually. Hopefully, this will help foster a culture in which students are trained to program effectively as a matter of course.

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