Molecular Ecology Notes published its first issue back in March 2001 – an issue containing a brief editorial, four technical notes, and 35 primer notes. The latter, brief papers describing new primer pairs useful for studying natural populations, have been the main output for the journal for the last twelve years: we have published almost 2,500 of them, and archived 35,000 primer pairs on the MER primer database.
A few things have happened in the last five years that have undermined the importance of primer notes (aka Permanent Genetic Resources Notes). First, in silico techniques and the wide availability of EST or Next Generation Sequence data mean that optimising 10-20 microsatellites is much easier than it used to be, and this was the primary reason behind our switch to the summary article format for primer notes at the start of 2009. Our ability to generate large volumes of sequence data has progressed very quickly, to the extent that microsats will soon be replaced by SNP and sequence data in many projects, with analyses based on individual assignment (e.g. paternity analysis) being the likely exception.
Given the declining importance of primer notes, and the existence of other good outlets (e.g. Cons. Gen. Resources and APPS), we will stop considering them for publication at the end of March 2013. This is the end of an era for ME Resources, but we feel it’s important to keep moving things forward.
We’re going to replace primer notes with the new Genomic Resources Notes. These stem from the recognition that many labs have unpublished NGS datasets, and together these have enormous value for the community. GR Notes will enable researchers to publish these without needing to incorporate them into a broader empirical study. As with primer notes, we will continue with the summary article format. However, as a typical GR note will contain four orders of magnitude more data than a primer note, the process of making the data publicly available becomes much more important. We have therefore decided to integrate Genomic Resources Notes with the review workflow on the Dryad database. This will work as follows:
1) authors will submit a brief GR Notes manuscript describing how the resource was developed and where the data can be accessed (the ms should be structured like a form);
2) we will email you a Dryad upload link;
3) any data or code from the paper not already archived elsewhere should be uploaded to Dryad – this could include reference files, sequence assemblies and data analysis pipelines.
4) the manuscript and the associated data will be assessed by an editor;
5) once accepted, the availability of the GR Notes paper and its data will be announced by the publication of a summary article listing all the notes accepted in that two month period.
Inclusion in the summary article will provide a way for the datasets to be found through standard literature searches, and the data themselves will then be available through public archives like NCBI’s Sequence Read Archive and Dryad. The accepted GR Notes manuscript itself will be included as a supplemental file on the summary article.
We’ve spent a few months working on this system, and we’re very keen to test it out, so please dust off those NGS datasets and send them in.