Automated analysis of ARISA data using ADAPT system – White Paper

This white paper was written by Robert in 2008 while working on different community profiling projets that combined microbiolgy and computer science.

The white paper describes a computational system consisting of the database ADAPTdb and the program ADAPT for the analysis of Automated Ribosomal Intergenic Spacer Analysis (ARISA) data sets. ARISA is a method for analyzing the composition of microbial communities that is both faster and cheaper than other community profiling techniques. In an application example, we describe the use of the tool for an unpublished data set and compare the results to work previously published using different analysis methods. Although there have been many papers until 2008 that used ARISA to analyze community samples, there were none that described computational approaches that allow the automatic analysis of the raw data sets. We have taken the manual process, automated it, and developed a web-based program for the automatic analysis, including taxonomic classifications, as well as autotrophic/heterotrophic and pathogenic/non-pathogenic comparisons.

This paper was submitted to BMC Bioinformatics and reviewed, but it was never published because of the comments that reviewer #2 made.

If this software is published in BMC Bioinformatics, this software will likely be used by many colleagues who will not look carefully at how ARISA works and doesn’t work. As a result, many analyses of microbial diversity will be highly flawed. Eventually, the community will learn the inaccuracy provided by the program but not before lots of scarce resources are spent and many meaningless papers are published.

That’s a pretty harsh criticism of their fellow microbial ecologists, who are apparently too stupid to understand their work and analyze their data.

Frankly, whoever wrote that review should be ashamed of themselves. Given comments like that there was no incentive for us to carry on making software that would mislead people, and so we never bothered.  The journal was not interested in publishing the paper, and we are not interested in helping people that are idiots.

Here are the complete reviews and the paper so you can decided for yourself. If you use ARISA, please cite this paper as:

Schmieder, R., Haynes, M., Dinsdale, E., Rohwer, F., and Edwards, R.A. Automated analysis of ARISA data using ADAPT system. 2009. http://edwards.sdsu.edu/research/adapt/

The ADAPT paper (1.4 MB).

reviewer #1 comments

Reviewer #2 comments