evogytis / fluB

Investigating the (co)evolution of reassorting influenza B lineages.
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Supplemental references #10

Closed trvrb closed 10 years ago

trvrb commented 10 years ago

Supplemental Figures and Tables should be directly referenced in the text, i.e. "Figure S1". Supplemental Figures and Tables should be reordered to reflect the order they are first referenced in the text. Ideally, all Supplemental Figures and Tables should be referenced from the main text, but this is not completely necessary. If Supplemental Figures and Tables are not referenced from the main text they should definitely be referenced from the supplemental text.

This is down the road a bit, but keep in mind eLife doesn't do supp. figures. I solved this by referencing what I would consider supp. figures from the Methods section that appeared at the end of the main text.

evogytis commented 10 years ago

Seems a bit odd that eLife don't do supplemental stuff. I'll cut down on some of the figures then. Stuff I think we should keep:

Stuff that can probably go:

I'll re-order the supp. figures after we've removed the ones we don't need.

trvrb commented 10 years ago

I presume much of the reason for this is to not bloat the manuscript with figures not central to the main narrative. The Nature paper with 50 supplemental figures can be difficult to make sense of.

I'd recommend keeping anything that can be directly (and usefully) referenced from the main text / narrative.

evogytis commented 10 years ago

I think keeping figures referenced in the text is the best idea. I'll do that. I don't think it's necessarily a bad idea to have loads of supplementary figures, I consider them as something you look up if you're not convinced by a figure in the main text.

evogytis commented 10 years ago

Closed via 72991bfce15d696dfefab502935cb07be3c64b58 ?

trvrb commented 10 years ago

Excellent. BTW you probably already noticed this, but rather than Supplemental Figures, eLife does Figure Supplements (heh). Like so: http://elife.elifesciences.org/content/2/e00631/F2

So, if there's more detail for a concept already expressed in the main figure it could work well as one of these.

evogytis commented 10 years ago

I haven't noticed that before, it looks really cool. I'll have a think about whether/what to include as figure supplements. That figure also reminds me - what shall we do about source code? I don't mind sharing the python code for processing trees (even though it's probably ugly as sin to experienced programmers) and the ipython notebooks for making the figures, but we can't share the sequences since they're from GISAID. Unless someone writes a script to select the same sequences we've used from the GISAID acknowledgement table, any source code included will be useful only to check that everything's coded up right rather than to reproduce the results. Or maybe I'm aiming too high.