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Guide Devil in the Details

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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 a similar analysis.


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Some in the field say that it should be enough to publish only the original data and final results, without providing detailed accounts of the steps in between. Others argue that it is pointless to document the version of the software used, as new incarnations of programs differ little.

But that is not always the case.

Devil in the Details: An Analysis of the Dark Side of the Self

Edward McCabe, then at the California NanoSystems Institute at the University of California, Los Angeles, was so perturbed when different versions of the same bioinformatics software gave wildly different results that he published a paper on it N. Henderson-Maclennan et al. Reviewers resisted its publication, asking what was new about the findings, as it was already common knowledge that different software versions could dramatically affect analyses.

There is a troubling undercurrent here: that the problem lies not with the lack of information, but rather with those who find the incomplete information a problem, such as researchers who are new to the field. Transparency is a laudable goal, but given the complexity of the analyses, is it realistic? There are certainly examples of stellar documentation.

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The Genomes Project, for example, a project to sequence and analyse more than a thousand genomes, has carefully detailed its workflows, and makes both its data and its procedures available for the world to see. It is perhaps easier for members of that project — which is essentially repeating the same procedure more than a thousand times — to practise good experimental hygiene than it is for individual scientists, who have more flexible and varied research goals.

Nevertheless, tools are coming online to simplify documentation of the complex analyses required for genome analysis. Neither of these is perfect, but they illustrate the level of detail that could enrich published reports. As genome sequencing spreads from the large, centralized sequencing centres that largely pioneered the technique into smaller labs and clinics, it is important that the community consider such solutions.

A Devil in the Details

Reprints and Permissions. Journal of Open Research Software Nature Methods By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate. Advanced search. Skip to main content. Subjects Authorship Genomics.

To ensure their results are reproducible, analysts should show their workings. Rights and permissions Reprints and Permissions. Comments By submitting a comment you agree to abide by our Terms and Community Guidelines. Download PDF.

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Allegory on the State of the Netherlands under Spanish Tyranny detail , Achenbach Foundation for Graphic Arts. Though unassuming at first glance, this finely engraved, detailed composition depicts ghoulish scenes of the Spanish Inquisition. Another ghoulish sight was the poor quality lining that was adhered to the back of the print.

The stiff lining paper was causing serious wrinkles and distortions in the art. In order to humidify and flatten the print and treat the stains and losses, the backing had to be removed. Testing showed that the lining adhesive was soluble in water, but that the oil-based printing ink was not, which allowed the print to be safely bathed in water.

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Tears were mended on the reverse with strips of Japanese tissue and wheat starch paste. Losses in the print were filled with dry cast paper pulp inserts. The cast paper pulp sheets are thin, soft, and pliable, making them a perfect material for repairing the handmade rag papers found in old master prints and drawings.

In this treatment, the cast paper pulp was also used to camouflage the appearance of adhesive stains and ink halos around the text, the results of old retouching. A thin layer of the cast pulp was carefully applied over stains and around the letters to make the lines appear crisper.