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Referencing Software – Summary

Jun 27, 2009

The post I wrote on June 11, Referencing Software, resulted in a rather lengthy thread on ICS-L, the Chemometrics discussion list. Most discussants generally agreed that the software used to develop results for scientific papers should be referenced, including the software title, publisher, year and version number.

There were a few dissenters. Sergey Kucheryavski wrote:

…it makes sense only in two cases.
1. The software implements some unique, patented methods that are not available in any other programs.
2. There is a special agreement (caused by special price [e.g. PLS toolbox for 100 USD] or some other benefits) between user and a software company.

In a similar vein, Richard Brereton wrote:

If however software has been bought (often at considerable cost) I do not think this obliges the originator to cite it, there is no ethical requirement, unless the software was purchased at a specially low price…

I find this to be a rather interesting concept and wonder what would happen if we applied it to books as well. If I paid the $1595 for Comprehensive Chemometrics by Brown, Tauler and Walczak, do I not have to reference it? How about Brereton’s “Applied Chemometrics for Scientists?” Do I have to reference it because it’s only $110? Or do I have to reference it only if I get a discount off the list price? Clearly this is ridiculous.

Most of the respondents felt that it was important to reference software in order to assure reproducibility of the work. Philip Hopke wrote:

It seems to me that the fundamental issue is the ability of the reader of a paper to be able to fully replicate the work that has been published. If work is not replicable, then it is not science. The issue then is what is required to ensure repeatability of the … work being reported.

And I agree that this is the most important issue, but it is not the only issue. Bruce Kowalski wrote:

If ya’ll want a real debate start taking issue with publications that don’t mention the first paper in a research area. There has always been a correct way to use references. What went wrong???????

Referencing the first paper in a research area is all about giving credit where it’s due. It’s not about reproducibility, (which, as Cliff Spiegelman observed, is often better served by referencing later work, often done by someone other than the original author). Likewise, referencing software is also partly about giving credit where it’s due–recognizing the effort expended to produce a useful tool of scientific value.