Abstract
‘Reproducible research’ has received increasing attention over the past few years as bioinformatics and computational biology methodologies become more complex. Although reproducible research is progressing in several valuable ways, we suggest that recent increases in internet bandwidth and disk space, along with the availability of open-source and free-software licences for tools, enable another simple step to make research reproducible. In this article, we urge the creation of minimal virtual reference environments implementing all the tools necessary to reproduce a result, as a standard part of publication. We address potential problems with this approach, and show an example environment from our own work.
Highlights
Replication of results is a central tenet of science; the idea that a meaningful result should be able to be replicated, and that publication should describe it in enough detail for this to be possible, motivates a large part of the basic activity of science
Reproducible research is progressing in several valuable ways, we suggest that recent increases in internet bandwidth and disk space, along with the availability of open-source and free-software licences for tools, enable another simple step to make research reproducible
Smith, Ventura et al [2] have given a comprehensive summary of these issues applied to analysis of mass spectrometry data, much of what they say is generally applicable to bioinformatics and computational biology
Summary
We believe strongly in this principle, we see some obstacles to its adoption, and we describe them below: Availability of data or code: some data are confidential, embargoed or restricted in access. All output from the reference environment should include citation information, and refer users back to the DOI or other identifier for the publication These obstacles are all genuine, but we feel that it is not at all a bad thing for barriers to replicating a result to be clearly stated as part of a publication. In the extreme situation that no aspect at all of a publishable result can be replicated in a reference environment for the reasons described above, it is valuable for that be clearly stated This situation is quite possible, we believe that it is not the norm in bioinformatics and computational biology, and it does not reduce the value of providing a reference environment for the majority of cases where it is not so. All of the barriers to making and distributing a reference environment are barriers to reproducing the research itself; where these barriers exist, they should be acknowledged in a publication
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