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swcarpentry / DEPRECATED-bc

DEPRECATED: This repository is now frozen - please see individual lesson repositories.
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Bioinformatics python capstone lesson #608

Open rbeagrie opened 10 years ago

rbeagrie commented 10 years ago

This lesson is intended to be a 1.5 hour demo that will sit at the end of a novice python bootcamp and show learners how to apply some of their new skills to bioinformatics. Currently work in progress, contributions/suggestions very welcome!

mitar commented 10 years ago

cc @janezd, @BlazZupan

shaunagm commented 10 years ago

What kind of feedback and suggestions are you looking for?

Also, what is the audience for the lesson? Presumably they won't all be genomics experts. It seems useful to provide some domain context and explanation for the example.

gvwilson commented 10 years ago

In this case we're assuming they are knowledgeable about genomics, but not about programming (or using software generally). Feedback on pace, organization, and intelligibility is most desired - the more specific the better.

drlabratory commented 10 years ago

I think some more explanation about the output of the various commands would help. The output of bedtools intersect loses me a bit. It's a hazard of bioinformatics: each program has its own output. I _think_ I know what the output means, but it would be better if the instructor reminded me.

rbeagrie commented 10 years ago

OK this is up to date with development as of now. Reviews very welcome!

rbeagrie commented 9 years ago

Just to clarify for anyone coming back to this PR, it's not ready for merging and needs some more work (which I'm planning to do after the Cambridge SWC bootcamp at the end of August). In the mean time, any more comments or contributions on the work so far would be very welcome.

gvwilson commented 9 years ago

@rbeagrie is this one good to merge? We'd like to clear things before #759.

rbeagrie commented 9 years ago

No, unfortunately this is not ready for merging. It needs maybe another half day of work and I've been struggling to find the time recently. Is there anything I can do to help smooth over #759? Should this be in it's own repo for example?

gvwilson commented 9 years ago

I think it's self-contained enough that you'll be able to redirect it to a new repo after the break, so shall we close the PR for now and you can resubmit in a couple of weeks?

rbeagrie commented 9 years ago

Yep, sounds good to me!