Scientific communication relies on evidence that cannot be entirely included in publications, but the rise of computational science has added a new layer of inaccessibility. Although it is now accepted that data should be made available on request, the current regulations regarding the availability of software are inconsistent. We argue that, with some exceptions, anything less than the release of source programs is intolerable for results that depend on computation. The vagaries of hardware, software and natural language will always ensure that exact reproducibility remains uncertain, but withholding code increases the chances that efforts to reproduce results will fail.
The rise of computational science has led to unprecedented opportunities for scientific advance. Ever more powerful computers enable theories to be investigated that were thought almost intractable a decade ago, robust hardware technologies allow data collection in the most inhospitable environments, more data are collected, and an increasingly rich set of software tools are now available with which to analyse computer-generated data.
However, there is the difficulty of reproducibility, by which we mean the reproduction of a scientific paper’s central finding, rather than exact replication of each specific numerical result down to several decimal places. We examine the problem of reproducibility (for an early attempt at solving it, see ref. 1) in the context of openly available computer programs, or code. Our view is that we have reached the point that, with some exceptions, anything less than release of actual source code is an indefensible approach for any scientific results that depend on computation, because not releasing such code raises needless, and needlessly confusing, roadblocks to reproducibility.
At present, debate rages on the need to release computer programs associated with scientific experiments2,3,4, with policies still ranging from mandatory total release to the release only of natural language descriptions, that is, written descriptions of computer program algorithms. Some journals have already changed their policies on computer program openness; Science, for example, now includes code in the list of items that should be supplied by an author5. Other journals promoting code availability include Geoscientific Model Development, which is devoted, at least in part, to model description and code publication, and Biostatistics, which has appointed an editor to assess the reproducibility of the software and data associated with an article6.
In contrast, less stringent policies are exemplified by statements such as7 “Nature does not require authors to make code available, but we do expect a description detailed enough to allow others to write their own code to do similar analysis.” Although Nature’s broader policy states that “...authors are required to make materials, data and associated protocols promptly available to readers...”, and editors and referees are fully empowered to demand and evaluate any specific code, we believe that its stated policy on code availability actively hinders reproducibility.
Much of the debate about code transparency involves the philosophy of science, error validation and research ethics8,9, but our contention is more practical: that the cause of reproducibility is best furthered by focusing on the dissection and understanding of code, a sentiment already appreciated by the growing open-source movement10. Dissection and understanding of open code would improve the chances of both direct and indirect reproducibility. Direct reproducibility refers to the recompilation and rerunning of the code on, say, a different combination of hardware and systems software, to detect the sort of numerical computation11,12 and interpretation13 problems found in programming languages, which we discuss later. Without code, direct reproducibility is impossible. Indirect reproducibility refers to independent efforts to validate something other than the entire code package, for example a subset of equations or a particular code module. Here, before time-consuming reprogramming of an entire model, researchers may simply want to check that incorrect coding of previously published equations has not invalidated a paper’s result, to extract and check detailed assumptions, or to run their own code against the original to check for statistical validity and explain any discrepancies.
Any debate over the difficulties of reproducibility (which, as we will show, are non-trivial) must of course be tempered by recognizing the undeniable benefits afforded by the explosion of internet facilities and the rapid increase in raw computational speed and data-handling capability that has occurred as a result of major advances in computer technology14. Such advances have presented science with a great opportunity to address problems that would have been intractable in even the recent past. It is our view, however, that the debate over code release should be resolved as soon as possible to benefit fully from our novel technical capabilities. On their own, finer computational grids, longer and more complex computations and larger data sets—although highly attractive to scientific researchers—do not resolve underlying computational uncertainties of proven intransigence and may even exacerbate them.
Although our arguments are focused on the implications of Nature’s code statement, it is symptomatic of a wider problem: the scientific community places more faith in computation than is justified. As we outline below and in two case studies (Boxes 1 and 2), ambiguity in its many forms and numerical errors render natural language descriptions insufficient and, in many cases, unintentionally misleading.
The failure of code descriptions
The curse of ambiguity
Ambiguity in program descriptions leads to the possibility, if not the certainty, that a given natural language description can be converted into computer code in various ways, each of which may lead to different numerical outcomes. Innumerable potential issues exist, but might include mistaken order of operations, reference to different model versions, or unclear calculations of uncertainties. The problem of ambiguity has haunted software development from its earliest days.
Ambiguity can occur at the lexical, syntactic or semantic level15 and is not necessarily the result of incompetence or bad practice. It is a natural consequence of using natural language16 and is unavoidable. The problem is regarded as so axiomatic that its avoidance or minimization is routinely taught at the undergraduate level in computing degrees. Nor is the study of ambiguity confined to the classroom. Active research continues on the use of tools for the detection of ambiguity17, the avoidance of ambiguity in major projects18, and the clarification of the intended functions of computer programs15.
One proposed solution to the problem of ambiguity is to devote a large amount of attention to the description of a computer program, perhaps expressing it mathematically or in natural language augmented by mathematics. But this expectation would require researchers to acquire skills that are only peripheral to their work (set theory, predicate calculus and proof methods). Perhaps worse, investment of effort or resources alone cannot guarantee the absence of defect19. A recent study20 of a tightly specified, short, simply expressed algorithm whose semi-mathematical specification was supplemented by example outputs showed that major problems still arose with large numbers of programs individually implemented to this specification. In short, natural language descriptions cannot hope to avoid ambiguous program implementations, with unpredictable effects on results.
Errors exist within ‘perfect’ descriptions
Let us assume for a moment that a researcher, perhaps trained—as are computer scientists—to think of computer algorithms as mathematical objects, and fully versed in the formal semantics of software description, has managed to describe a computer program perfectly in some notation. Unfortunately, even such a description would not ensure direct or indirect reproducibility, because other forms of error or ambiguity (unrelated to natural language) are likely to creep in, leading to potentially serious uncertainties (Box 2).
First, there are programming errors. Over the years, researchers have quantified the occurrence rate of such defects to be approximately one to ten errors per thousand lines of source code21.
Second, there are errors associated with the numerical properties of scientific software. The execution of a program that manipulates the floating point numbers used by scientists is dependent on many factors outside the consideration of a program as a mathematical object22. Rounding errors can occur when numerous computations are repeatedly executed, as in weather forecasting23. Although there is considerable research in this area, for example in arithmetic and floating point calculations24,25,26,27, algorithms28, verification29 and fundamental practice30, much of it is published in outlets not routinely accessed by scientists in generic journals, such as Computers & Mathematics with Applications, Mathematics in Computer Science and the SIAM Journal on Scientific Computing.
Third, there are well-known ambiguities in some of the internationally standardized versions of commonly used programming languages in scientific computation13. Monniaux22 describes an alarming example relating to implementation of software features:
“More subtly, on some platforms, the exact same expression, with the same values in the same variables, and the same compiler, can be evaluated to different results, depending on seemingly irrelevant statements (printing debugging information or other constructs that do not openly change the values of variables).”
This is known as an order-of-evaluation problem and many programming languages are subject to its wilful ways. Ironically, such execution ambiguity is quite deliberate and is present to allow a programming language compiler more flexibility in its optimization strategy. And even when programs are simple, or developed by the largest software companies, such errors remain surprisingly common: numerical ambiguity led Microsoft to declare in 2010 and reaffirm in September 2011, that the treatment of floating point numbers in its popular Excel spreadsheet “...may affect the results of some numbers or formulas due to rounding and/or data truncation.” (http://support.microsoft.com/kb/78113).
Perfection is no guarantee of reproducibility
Finally, even if a computer program could be unambiguously described and implemented without error, other problems can arise in machine deployment whereby the results from identical code often diverge when hardware and software configurations are changed22. So even perfection in one’s own software environment does not guarantee reproducibility. As a result, to maximize the chances of reproducibility and consistency, not only would we urge code release, but also a description of the hardware and software environment in which the program was executed and developed.
Challenges are no excuse for closed code
Nature’s policy on code release implies that algorithmic descriptions using mathematical specifications, equations, formal algorithmic descriptions or pseudocode (simplified version of complete code) may be required. But there is no guarantee that such tools can avoid ambiguity20, and even if they could, we have shown above that implementation and numerical errors—possibly compounded by differences in machine architecture—will still arise. So, even if complete code is made available, exact replication or even reproduction of central results may fail. A reasonable observer might therefore ask why code should be made available at all. Our response is that the alternative is far worse. Keeping code closed ensures that potential uncertainties or errors in a paper’s conclusions cannot be traced to ambiguity, numerical implementation, or machine architecture issues and prevents testing of indirect reproducibility. Although it is true that independent efforts to reproduce computational results without recourse to the original source code constitute an important approach, the all-too-common treatment of code as a black box unnecessarily slows and impedes valid efforts to evaluate model results. We therefore regard the non-availability of code as a serious impediment to reproducibility.
Potential barriers and proposed solutions
There are a number of barriers to the release of code. These include a shortage of tools that package up code and data in research articles; a shortage of central scientific repositories or indexes for program code; an understandable lack of perception of the computational problems with scientific code leading to the faulty assumption that program descriptions are adequate (something we address in this article); and finally that the development of program code is a subsidiary activity in the scientific effort.
A modest proposal
An effective step forward would be for journals to adopt a standard for declaring the degree of source code accessibility associated with a scientific paper. A number of simple categories illustrate the idea:
• Full source code: full release of all source code used to produce the published results along with self-tests to build confidence in the quality of the delivered code, as is the case with Perl modules in the CPAN archive, for example (http://cpan.org).
• Partial source code: full release of source code written by the researcher accompanied by associated documentation of ancillary packages used, for example commercial scientific subroutine libraries.
• Marginal source code: release of executable code and an application programming interface to allow other researchers to write test cases.
• No source code: no code at all provided.
This hierarchy of disclosure would alert both the readers and authors of a journal article to the fact that the issue is important and would highlight the degree to which results might be reproduced independently. There remain, however, some potential stumbling blocks, a number of which can easily be resolved using existing facilities.
Intellectual property rights
Clearly, if there is evidence of commercial potential or use, such as a patent or some copyright, then there is a problem. It is difficult to see how a journal might deal with this without substantial financial commitment to independent testing under a non-disclosure agreement or possibly even the purchase of commercial rights. Perhaps the simplest solution is for a journal to flag the software as ‘No source code’ (ideally giving the reasons) until such time as the source code can be included, either because the code goes into the public domain or is released under some free licence. Such a designation simply says that, for the moment, the results are not reproducible with the authors’ own source code, and that testing of the main results must proceed with independent approaches.
Researchers may not have access to at least some of the software packages that are used for development. We suggest that this would not be a problem for most researchers: their institutions would normally provide such software. If it were to be a problem, then a journal could mark a publication as ‘Partial source code’. The release of the code, even without the software environment required for compilation and execution, would still be valuable in that it would address issues such as dissection and indirect reproducibility (see above) and would enable rewriting using other programming languages.
Adopting the simple disclosure of the availability of source code will help make it clear to the readership of a journal that this is an important issue, while also giving them an idea of the degree of code release. However, we would further suggest that journals adopt a standard that specifies that supplementary material supporting a research article must describe each of the released modular components of any software used. Nature editors and referees are already empowered to include an appraisal of code in their judgement about the publication potential of the article, and this practice should be more widely advertised and supported. A good example of this approach is the way that the journal Geoscientific Model Development asks authors to describe their program code.
Over the past two decades, the open-source community has solved the logistics of releasing and storing code while maintaining a cooperative development environment. SourceForge (http://www.sourceforge.net/) is an excellent example. Founded in 1999, it is a web-based source-code repository which acts as a free centralized location for developers working on open-source projects. It currently hosts around 300,000 projects and has over two million registered users. Not only does it store source code but also it provides access to version control information, project wikis (websites that are easily modifiable by its users) and database access. We urge funding agencies to investigate and adopt similar solutions.
There are a number of tools that enable code, data and the text of the article that depends on them to be packaged up. Two examples here are Sweave associated with the programming language R and the text-processing systems LaTeX and LyX, and GenePattern-Word RRS, a system specific to genomic research31. Sweave allows text documents, figures, experimental data and computer programs to be combined in such a way that, for example, a change in a data file will result in the regeneration of all the research outputs. GenePattern-Word RRS is similar in that it enables an author to link text, tables and figures to the analysis and data that yielded the results, reported in a word-processed document; it also allows further experimentation (for example, additional analyses can be carried out). It is still early days, however, and localized solutions are emerging at the grassroots level. Donoho and co-workers, for example, have developed software packages that allow anyone with access to the Matlab programming language and development environment to reproduce figures from their harmonic analysis articles, inspect source code, change parameters and access data sets32.
Steps to implementation
Our thesis is that journal and funding body strictures relating to code implementations of scientific ideas are now largely obsolete. We have suggested one modest path to code availability in this article. There are a number of further steps that journals, academies and educational organizations might consider taking:
• Research funding bodies should commission research and development on tools that enable code to be integrated with other elements of scientific research such as data, graphical displays and the text of an article.
• Research funding bodies should provide metadata repositories that describe both programs and data produced by researchers. The Australian National Data Service (http://www.ands.org.au/) which acts as an index to data held by Australian research organizations, is one example of this approach.
• Journals should expect researchers to provide some modular description of the components of the software that support a research result; referees should take advantage of their right to appraise software as part of their reviewing task. An example of a modular description can be seen in a recent article published in Geoscientific Model Development33.
• Science departments should expand their educational activities into reproducibility. Clearly such teaching should be relevant to the science at hand; however, courses on statistics, programming and experimental method could be easily expanded and combined to include the concept of reproducibility.
We thank D. Hales of the Department of Design at the Open University and P. Piwak of the Department of Computing for pointing out some reproducibility work outside computing. J.G.-C. is grateful to I. Goz for pointing out the calculation errors in the CRUTEM data from the Meteorological Office.
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BMC Bioinformatics (2017)