search

krassowski / multi-omics-state-of-the-field

Analyses for "State of the field in multi-omics research: from computational needs to data mining and sharing"
https://doi.org/10.3389/fgene.2020.610798
MIT License
24 stars 13 forks source link

Prepare repository for referencing in the manuscript #22

Closed krassowski closed 3 years ago

krassowski commented 4 years ago
  1. [ ] Clean up notebooks (partially done, ideally the parsing and plotting code would be moved out of notebooks)
    • [x] Maybe move notebooks/code out of the root of repository to avoid clutter
  2. [x] Move anything which was not referenced in the manuscript to a different branch
  3. [x] Point out readers/reviewers to specific file/notebooks
  4. [x] Split "Overview" notebook to "Exploration" (the first part) and "Overview" ("Overview_figure"? - second part)

After hearing back from the reviewers (i.e. knowing if the version is final):

  1. [x] Branch out/tag a release (and put it in the manuscript)
  2. [x] Prepare a binder to allow for interactive exploration (the code dataset is <15MB so we can host it, but probably not in the repo, but in a dedicated data archive)
krassowski commented 4 years ago

Also, the (compressed) downloaded dataset is only 17 MB, we could push it and make the overview notebook interactive.

vd4mmind commented 4 years ago

@krassowski yes, but that can be done a bit later. My current go-to will finish what we have to sent to Biswa to built the comprehensive manuscript package. Preparing of the repo can be done once we are nearing submission.

krassowski commented 4 years ago

Yes, I know. I opened the issue extracting the earlier discussion from a closed PR so that I do not have to do this right now and I can remember to do this later ;)