Paper format and journal

[jeromekelleher]

The paper is envisaged as a description of msprime all of the features that it has, with comprehensive references to the literature of existing simulators, to emphasise msprime's large feature set and fragmented state of the simulation ecosystem.

Some options:

Bioinformatics application note

A bioinformations application note is a pretty standard format for software papers like this. It would be hard to argue against publishing this paper in Bioinformatics, given the number of simulators that are already published in this format.

The downside is the format is very short. My current, very incomplete, draft is already longer than this. Given the number of references and the number of authors, I think it would be very terse indeed.

Heredity computer note

Heredity have recently launched a computer note format which might be appropriate.

[fbaumdicker]

Given the number of new features, Heredity sounds appropriate to me.

Other alternatives might be:

BMC Bioinformatics Briefings in Bioinformatics PLOS Computational Biology GigaScience Nucleic Acids Research

[andrewkern]

I'd also throw G3 into the mix. They are fully OA, very good to deal with, and generally a nice journal IMO

[molpopgen]

I second G3

[jeromekelleher]

Thanks for the input. I think we want to go somewhere where there's an explicit "software paper" stream. Do G3 have this?

[hugovk]

Another option is the Journal of Open Source Software, JOSS.

Here's an example submission:

• https://github.com/fatiando/pooch/pull/116
• https://github.com/openjournals/joss-reviews/issues/1928
• https://github.com/openjournals/joss-reviews/issues/1943
• https://joss.theoj.org/papers/10.21105/joss.01943

[jeromekelleher]

Good idea, thanks @hugovk. I think we'd probably weight more towards a biology journal to get the attention of potential users, but it's a good option.

[molpopgen]

Thanks for the input. I think we want to go somewhere where there's an explicit "software paper" stream. Do G3 have this?

Yep. https://www.g3journal.org/content/article-types#software

[jeromekelleher]

OK, G3 it is for now. We can revisit later if needs be.

[sgravel]

I'll also suggest the Methods, Technology, and Resources section at Genetics. I think the manuscript could be a good fit there, and could always be forwarded with reviews to G3 if needed. Even though it a delayed OA journal, there is an instant OA option as well.