High-Level Goals for Publication

[mneinast]

What should a published manuscript for TraceBase / version of TraceBase include?

required

• upload peak annotation data
• download collated results in uniform formats
• upload mzXML
• download mzXML
• a new public instance of tracebase, accessible to anyone, hosted at princeton
• anyone can install tracebase and run their own server
• updated documentation
• polish of existing features

considering

• support automated data
  • this could be a simple "workaround" support, based on identifying the type of PeakAnnotation file, or it could be something more in-depth
• shiny app for browsing data downloaded from tracebase (ie https://github.com/MRMacArthur/TracebaseView)

save for after publication, if ever

• "unknown" peaks

[hepcat72]

I'll propose some rough draft item breakdowns... and I'll think about these as I handle the milestone editing.

• download mzXML
  • the bulk download PR is currently in the review process and working on dev (I think it's on the branch that's on there now)
  • There are a number of extant issues for both display and download of mzXML files in other views
• a new public instance of tracebase, accessible to anyone, hosted at princeton
  • Probably fixing of data issues on the rabinowitz repo would fall here. I'll create a publication milestone on that repo
• anyone can install tracebase and run their own server
  • Contrib doc needs updating
  • We should add a note, perhaps in the footer, about citing tracebase. I forget the name of those software citations you can create. We did it for TreeView. I'll have to look in my notes.
• updated documentation
  • Code documentation
    • The handling of errors by the AggregatedErrors class needs more documentation
    • MaintainedModel needs more documentation
    • The advanced search "formats" need more documentation
  • Usage documentation
    • This is the "current" TraceBaseDocs
  • Curator documentation
    • We essentially need a generalized version of what's in nplcadmindocs
• polish of existing features
  • Bug fixes
  • Aesthetic display issues (typos, consistent headers, etc)
  • Slowness / timeouts
  • Optimization (loading speed)
  • Tests (convert tests from legacy code to current code)