PeerJ CS submission guidelines

This is for the jax-unirep paper.

https://peerj.com/about/policies-and-procedures/#discipline-standards

PeerJ welcomes articles describing bioinformatics software tools. These articles should present new software tools (or significant new functionality in existing software) of particular interest to the bioinformatics and/or computational biology communities. The described tools should provide new computational or analytical functionality for researchers.

The functionality of the software should, where appropriate, be validated using real-world biological data and/or compared to existing tools. If available as a package (e.g. Python, R, Matlab, Octave), it should be accompanied by a minimal script that downloads the data (if not included in the package), loads it, and performs the analysis to reproduce the results (tables, plots, visualizations etc.) in the manuscript. Documentation & comments must be clear and sufficient to allow a typical user to perform the analysis described in the article. Ideally, the tools should be usable in a workflow that encourages reproducible research practices.

The software must be released under an open source license (e.g. MIT, GPL) and be widely available (i.e. hosted in a public repository such as Github or Bitbucket, or an institutional repository). Use of a version control system (e.g. Git, Subversion etc.) is strongly encouraged, as is adherence to language-specific packaging practices where appropriate. We also recommend the inclusion of appropriate unit tests. The software must be free to noncommercial users, and must be accessible without requiring any personally identifiable information. Software and validation data sets must comply with PeerJ Data and Materials Sharing policies. Reliance on a proprietary software such as Matlab does not preclude the publication but in general, a fully open source method is to be preferred.

The guidelines are good. Scope is right. I say we go for it.

jax-unirep

Key Information

Open PRs

Paper

  • Next place to submit to: PeerJ Computer Science. (see: PeerJ CS submission guidelines)
  • Other locations in consideration: JCIM Application Notes
  • Rejected at:
    • Bioinformatics
    • JMLR-MLOSS

The main uses of jax-unirep

The main use of jax-unirep really is in getting "standardized" representations of proteins that can be used for downstream ML applications easily.