[x] add version control point to project management introduction
[ ] cite books (Vince Buffalo, PRFB, etc - titus says there are 3-4). I think it might be best to call attention to them as further resources - maybe in the troubleshooting section? Sentence with refs or table with refs + brief description. Think table might be better (title: Additional Resources(?))
re: ryan convo: " your local HPC might be unprepared for sophisticated massive users (the Lisa effect)"
[x] In intro or workflows(?), ~ 1 sentence:
a lot of bioinformatics is converting between formats and conveying info between tools. Maybe mention that "decisions are made at every level of compute, and even if workflows “just” cobble together other software in a simple way, there are lots of implicit assumptions made there."
[x] troubleshooting section? 1 sentence:
known knowns and known unknowns are possible to evaluate fairly rigorously, I think, because you have a good idea of what to look for. there’s still some guesswork involved because you have to focus in on a sensible range of parameters and who knows what “sensible”?
unknown unknowns, like the unintended consequences of filtering for metadata and joins across different programs, are MUCH harder to track down and evaluate. well, and also the impact of bugs from the software you’re using as well as your own pipeline.
[x] in workflows or troubleshooting: (1 sentence?)
"There’s a massive difference between production workflows that can be run at scale and that almost never fail without a useful error message, vs research workflows that are run on a dozen samples and can have edge cases. Often the edge cases in research pipelines clue you into where interesting stuff is, either technically tricky OR biologically weird."
[x] Conclusion, maybe discuss:
"I think there is a new breed of biologist/bioinformatician coming along (echoing something Mick Watson said on Twitter). These workflow-enabled biologists will become increasingly valuable as data set size and complexity increases, along with the associated tool chain. Very few people are training them (waves hi! :)""
Choosing a workflow: talk about nextflow, cwl without bringing up scaling differencesWorkflowssection:[x] in workflows or troubleshooting: (1 sentence?)
[x] Conclusion, maybe discuss:
[ ] Make abstract and intro less technical