QoL: Auto-Generated Methods Pipelines?

[borsta]

Something I’ve been thinking about for awhile that is purely a QoL request. It would be really useful if cryoSPARC could auto-generate a .txt ‘data processing pipeline’ file for jobs marked as “final.” The output could include job types in order, particle counts at each stage, the percentage/number of particles carried forward, and any custom parameters used.

This would be used primarily for make writing methods sections for manuscripts much easier and help standardize reporting, since methods are sometimes written sparsely and miss important details that impact reproducibility.

[rbs_sci]

Something like this has been requested in the past, I’m pretty sure. Anyway, it would be useful.

Dumping out PNG or PDF files of final output from different jobs (as relevant) might be useful also (e.g. representative mic, CTF fit for same, picks on it, 2D classes selected, etc…)

@borsta

…since methods are sometimes written sparsely and miss important details that impact reproducibility.

I could say quite a lot on this point, but I’ll summarise it as “Damned if you do, damned if you don’t.”