Where can I publish a small paper on my pipeline and methods?

[Genomics101]

Greetings.

I have some material for a simple and very small, but useful, paper (described below). However, I have no idea where to publish it because all the journals I know are quite "big" - e.g. Bioinformatics, PLoS Computational Biology, Genome Research.

The paper is aimed at non-experts who work on my particular group of organisms or ones like it (medium-sized haploid and/or AT-rich genomes). The basis of the paper is that, using my results and shell scripted pipeline with a quick UNIX tutorial, any biologist can map and assess variants in a genome in way that is quick and light-weight and does not require the use of a web interface; they can do it like "real" bioinformaticians: fast, flexibly, and iteratively.

Basically, I have an assembled shell script that can be slightly modified for several different types of analyses, and outputs specially formatted results for what we would be looking for. The real trick is that it uses common tools (e.g. SAMtools, BFCtools) that are really for human (i.e. diploid and balanced AT) genomes and makes them effective tools for other organisms. I have tested all the different parameters and found the best ways to effectively find variants, which is different for these genomes from standard practices. There is nothing too revolutionary about this, but I definitely think it is a useful tool for people to set up their own pipelines and start to do the mapping in an intelligent way.

The work comes out of spending a year as a bioinformatics person and an experimental biologist at a medical research institution where people are really scared to work on a cluster or do anything command-line driven. I've taught the pipeline to plenty of people now and it seems to be working well.

Apologies if this is not the correct forum to search for guidance on this topic, I will happily switch if someone directs me to the correct place. Cheers and thanks.

[aaronh]

PloS One might be a great place for this.

[jimmybee]

Theres always arXiv print server

http://arxiv.org/

[chadn737]

arXiv is for pre-prints, I think it is a great idea, but you would still want to submit to an actual journal.

I would check out some of the BioMed journals, there is a variety and one of them may fit your paper. A better choice might actually be a journal that focuses on the sorts of organisms your pipeline targets, as opposed to a Bioinformatics journal. This would make it more likely to be read by the sort of audience you indicated it is meant for.

[gsgs]

post it on your webpage and/or this or another forum.

And take care that the useful keywords are included, so
people interested in the topic will find it with search engines

[yl01]

Source Code for biology and medicine could be an option.

[Gig77]

BMC Research Notes

[tayebwajb]

Write to the Publications Manager of PLoS Computational Biology; [email protected]. They are always very interested to hear suggestions for new articles. They have published a series of "perspective" articles and I am sure they will let you know how your article may fit in.

I am also working with a group of biologists who are command-line shy and I would find your script very useful. Is it possible to grant me advance access to your shell script or may be a preprint of your article? You may send it to Johnbosco.Tayebwa[at]med.lu.se

[Simon Anders]

What about BMC Bioinformatics?

Note that their instructions to authors state

"BMC Bioinformatics is an open access, peer-reviewed journal that considers articles on all aspects of the development, testing and novel application of computational and statistical methods for the modeling and analysis of all kinds of biological data, as well as other areas of computational biology.

It is journal policy to publish work deemed by peer reviewers to be a coherent and sound addition to scientific knowledge and to put less emphasis on interest levels, provided that the research constitutes a useful contribution to the field."

In other words, they won't reject you only because your work is of interest to only a restricted community, as long as it is sound.

[frozenlyse]

Bioinformatics has a short 2 page article type (Application Note) which sounds like it suits your pipeline well.

[Setfelix]

Hi Genomics101, where did you eventually publish your pipeline and methods?
I also have a shell-scripted pipeline I would like to publish.

Thanks.