Hi, everyone
I hope you are all well!
I have a few concerns and comments related to our manuscript that I would like to raise as issues, so that we can discuss them and, if necessary, address them prior to the submission of our manuscript for consideration for publication in a peer-reviewed journal.
Concern
In this issue, I would like to comment on the apparent lack of domain-specific contextualized usage of GitHub in the manuscript.
While we frequently use the term “ecology and evolutionary biology” (EEB) to help cater our manuscript to our choice of public, most of the applications that we explicitly provide are non-EEB specific.
There are a few examples in the use cases [e.g., the R packages in the “Peer review” section, and some places where we discuss laboratories (but note that there are laboratories in non-EEB fields)].
It is great (and natural) that we have content that can be used by researchers in other domains. However, I feel that more domain-specific applications of the usage of GitHub can help our readers and researchers in ecology and evolution reflect better on how they can use GitHub in their hands-on research projects. Ultimately, the journals we are aiming at are specific to ecology and evolution, and I fear that reviewers and editors might express concerns about this in the initial parts of the review process.
I acknowledge our challenges in trying to contextualize this super broad tool to EEB researchers, as well as our limitations with the text length. Some of the applications we discuss would not require this type of specificity (e.g., manuscript writing).
Proposed solution
A potential solution that I see to adjust for this perception is to include more field-specific applications for GitHub across the text, such as examples of usage with long-term ecological studies, sequencing and assembly of genetic databases, simulations of communities or metacommunities and their applications in theoretical and empirical studies.
For example, the automated near-term iterative forecasting systems that have been developed for the long-term ecological study in Portal (Arizona, US; https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.13104). Another example could be the reproducible pipeline for the study by Kazelles et al. (2019, Global Change Biology; https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.14829), which has an automated pipeline and a binder associated (https://github.com/McCannLab/HomogenFishOntario) with the GitHub repository that automatically runs and reproduces the analyses and figures that are published in their study.
Please let me know what you think about this concern, if you have a proposition, and (if needed) if you could help with some of the additions to the manuscript.